3OPS | pdb_00003ops

Crystal structure of mandelate racemase/muconate lactonizing protein FROM GEOBACILLUS SP. Y412MC10 complexed with magnesium/tartrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N4F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.2 M MG CHLORIDE, 0.1 M TRIS-HCL, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.989	α = 90
b = 66.375	β = 96.59
c = 154.854	γ = 90

Symmetry
Space Group	C 1 2 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		2010-08-19		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

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	77.6	0.13	3.6	2.5		83601

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	2.03	54		0.959		1.7	2859

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 (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	3N4F	2.2	20	67849	3428	82.52	0.2321	0.2279	0.23	0.3106	0.31	RANDOM	38.2209

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]
0.38		-0.3	-0.35		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.34
r_dihedral_angle_3_deg	17.817
r_dihedral_angle_4_deg	16.799
r_scbond_it	7.14
r_dihedral_angle_1_deg	6.023
r_mcangle_it	3.041
r_angle_refined_deg	1.281
r_mcbond_it	0.653
r_scangle_it	0.549
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.34
r_dihedral_angle_3_deg	17.817
r_dihedral_angle_4_deg	16.799
r_scbond_it	7.14
r_dihedral_angle_1_deg	6.023
r_mcangle_it	3.041
r_angle_refined_deg	1.281
r_mcbond_it	0.653
r_scangle_it	0.549
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12094
Nucleic Acid Atoms
Solvent Atoms	935
Heterogen Atoms	58

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	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.