2HAG | pdb_00002hag

Crystal structure of a putative dyp-type peroxidase protein (so_0740) from shewanella oneidensis at 2.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	5.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.31	α = 90
b = 94.31	β = 90
c = 113.68	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-04-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979291, 0.918370, 0.978940	SSRL	BL11-1

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	2.75	29.54	95.4	0.107	10.85			13932			58.902

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	2.75	2.85	86.7		0.835	1.7		2297

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.75	29.54	13888	691	99.72	0.193	0.191	0.2	0.229	0.24	RANDOM	58.485

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]
-2			-2		3.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.04
r_dihedral_angle_3_deg	15.824
r_dihedral_angle_4_deg	12.404
r_dihedral_angle_1_deg	6.927
r_mcangle_it	3.803
r_scangle_it	3.761
r_mcbond_it	2.67
r_scbond_it	2.574
r_angle_refined_deg	1.134
r_angle_other_deg	0.615
r_mcbond_other	0.532
r_nbd_refined	0.228
r_symmetry_vdw_other	0.215
r_nbd_other	0.212
r_symmetry_hbond_refined	0.203
r_nbtor_refined	0.198
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.146
r_nbtor_other	0.093
r_chiral_restr	0.063
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2453
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing
RESOLVE	phasing