3T9P | pdb_00003t9p

Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme family protein from Roseovarius

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M NaCL, 0.1M HEPES pH 7.5, 1.6M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.594	α = 90
b = 91.362	β = 90
c = 100.271	γ = 90

Symmetry
Space Group	P 21 21 21

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	mirrors	2011-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.08	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	1.97	50	99.9	0.059	12.5	12.9	71641	71641

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	1.97	2.04	100		0.233	5	12.6	7073

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3T8Q	1.97	46.99	71641	67733	3617	99.58	0.1826	0.18066	0.19	0.21907	0.22	RANDOM	21.53

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]
-0.03			0.07		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.076
r_dihedral_angle_4_deg	16.164
r_dihedral_angle_3_deg	13.731
r_dihedral_angle_1_deg	6.98
r_scangle_it	5.853
r_scbond_it	3.852
r_mcangle_it	2.31
r_angle_refined_deg	2.179
r_mcbond_it	1.465
r_chiral_restr	0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.076
r_dihedral_angle_4_deg	16.164
r_dihedral_angle_3_deg	13.731
r_dihedral_angle_1_deg	6.98
r_scangle_it	5.853
r_scbond_it	3.852
r_mcangle_it	2.31
r_angle_refined_deg	2.179
r_mcbond_it	1.465
r_chiral_restr	0.178
r_bond_refined_d	0.031
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5679
Nucleic Acid Atoms
Solvent Atoms	620
Heterogen Atoms	32

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

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.