2A4A | pdb_00002a4a

Deoxyribose-phosphate aldolase from P. yoelii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JCL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	298	PEG4K, Tris pH 8.5, NaCl 0.2 M, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.17	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.121	α = 90
b = 143.472	β = 106.24
c = 50.156	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	SBC-3		2005-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	1.85	34.68	98	0.68	20.3	3.5		41400		-3

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)
1	1.85	1.92	87.2		0.501	1.56	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	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	1JCL	1.84	34.68	41400	39307	2092	97.34	0.20503	0.2028	0.2	0.2483	0.25	RANDOM	33.875

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]
-0.25		-0.23	-1.12		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.56
r_dihedral_angle_3_deg	13.948
r_dihedral_angle_4_deg	12.231
r_dihedral_angle_1_deg	5.935
r_scangle_it	3.951
r_scbond_it	2.748
r_mcangle_it	2.115
r_mcbond_it	1.378
r_angle_refined_deg	1.147
r_nbtor_refined	0.299
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.08
r_symmetry_hbond_refined	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3906
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing