2BDZ | pdb_00002bdz

Mexicain from Jacaratia mexicana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YAL	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci
experimental model	PDB	1GEC	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci
experimental model	PDB	1PPO	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci
experimental model	PDB	1MEG	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci
experimental model	PDB	1PCI	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10	293	20 % (w/v) PEGl 6000, 0.1 M citrate, 15 % (v/v) ethanolamine, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.356	α = 90
b = 90.454	β = 92.636
c = 80.391	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Nonius Kappa CCD		2003-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	40.8	99.3	0.095	17.271	5.9		47249

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	97.1	97.1	0.296	3.495	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci	2.1	40.8	40977	4576	95.51	0.183	0.177	0.1813	0.238	0.175	RANDOM	14.046

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.66		-0.27	1.05		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.388
r_dihedral_angle_4_deg	18.847
r_dihedral_angle_3_deg	12.555
r_dihedral_angle_1_deg	6.222
r_mcangle_it	1.819
r_scangle_it	1.801
r_scbond_it	1.3
r_mcbond_it	1.235
r_angle_refined_deg	1.092
r_nbtor_refined	0.301
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.128
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6472
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing