3CYJ | pdb_00003cyj

Crystal structure of a mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100mM Bis-Tris pH 6.5, 1.4M Ammonium phosphate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.1	α = 90
b = 193.1	β = 90
c = 113.483	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	MAR CCD 165 mm		2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	48.28	98.4	0.16	0.16	8.5	10.4	93498	93498			34.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	98.3		0.431	0.431	3.5	10.3	13481

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.3	20	93295	93295	4684	98.2	0.245	0.243	0.25	0.292	0.3	RANDOM	43.459

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]
-0.06			-0.06		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.975
r_dihedral_angle_4_deg	17.034
r_dihedral_angle_3_deg	15.084
r_dihedral_angle_1_deg	6.215
r_scangle_it	4.9
r_scbond_it	3.037
r_mcangle_it	1.685
r_angle_refined_deg	1.676
r_mcbond_it	0.89
r_chiral_restr	0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.975
r_dihedral_angle_4_deg	17.034
r_dihedral_angle_3_deg	15.084
r_dihedral_angle_1_deg	6.215
r_scangle_it	4.9
r_scbond_it	3.037
r_mcangle_it	1.685
r_angle_refined_deg	1.676
r_mcbond_it	0.89
r_chiral_restr	0.105
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10768
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	14

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.