3MMH | pdb_00003mmh

X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.25	293	23% MPD, 120 mM Mg(CH3COO)2, 100 mM cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.32	α = 104.17
b = 39.48	β = 105.16
c = 52.25	γ = 100.5

Symmetry
Space Group	P 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	ADSC QUANTUM 315r		2008-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.886	SOLEIL	PROXIMA 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	1.2	25	84.4	0.039	19.91	8.54		75066		-3	18.941

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	1.23	37.4		0.418	3.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.25	20	70912	3545	100	0.12	0.118	0.1288	0.157	0.1626	RANDOM	19.68

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]
0.3	0.09	0.08	-0.03	0.01	-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.659
r_dihedral_angle_4_deg	17.203
r_dihedral_angle_3_deg	12.176
r_dihedral_angle_1_deg	7.406
r_scangle_it	6.8
r_scbond_it	5.065
r_mcangle_it	3.516
r_mcbond_it	2.488
r_angle_refined_deg	2.286
r_rigid_bond_restr	2.258

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.659
r_dihedral_angle_4_deg	17.203
r_dihedral_angle_3_deg	12.176
r_dihedral_angle_1_deg	7.406
r_scangle_it	6.8
r_scbond_it	5.065
r_mcangle_it	3.516
r_mcbond_it	2.488
r_angle_refined_deg	2.286
r_rigid_bond_restr	2.258
r_angle_other_deg	1.24
r_mcbond_other	0.865
r_chiral_restr	0.285
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2564
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	69

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.