3M13 | pdb_00003m13

Crystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	20% PEG4000, 200 mM sodium acetate, 100 mM Tris HCL, pH 8.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.296	α = 90
b = 69.298	β = 93.4
c = 111.427	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	ADSC QUANTUM 315				SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90	APS	14-BM-C

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	40	95.3	0.072	21	5.9		83978

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	2.18	96		0.475	3.2	5.1

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	2.1	29.2	83762	4212	94.87	0.19	0.187	0.19	0.248	0.25	RANDOM	37.122

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.681
r_dihedral_angle_4_deg	19.025
r_dihedral_angle_3_deg	16.715
r_dihedral_angle_1_deg	7.275
r_scangle_it	4.624
r_scbond_it	3.074
r_angle_refined_deg	1.984
r_mcangle_it	1.884
r_mcbond_it	1.123
r_chiral_restr	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.681
r_dihedral_angle_4_deg	19.025
r_dihedral_angle_3_deg	16.715
r_dihedral_angle_1_deg	7.275
r_scangle_it	4.624
r_scbond_it	3.074
r_angle_refined_deg	1.984
r_mcangle_it	1.884
r_mcbond_it	1.123
r_chiral_restr	0.14
r_bond_refined_d	0.023
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11912
Nucleic Acid Atoms
Solvent Atoms	497
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.