3MQT | pdb_00003mqt

Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Shewanella pealeana

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.1M MgCl2, 0.1M Tris, pH 8.5, 30% PEG 4K, Dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.164	α = 98.47
b = 146.142	β = 96.8
c = 158.71	γ = 105.04

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 315	mirrors	2010-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	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	2.1	50	89	0.12	6.7	5.1	484982	484982

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)
	2.1	2.18	46		0.62	2	3.6	25144

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	3MKC	2.1	49.33	484982	478270	4843	100	0.18554	0.18526	0.1886	0.21318	0.2175	RANDOM	19.086

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]
-0.26	-0.86	-0.15	0.28	0.42	-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.655
r_dihedral_angle_3_deg	16.691
r_dihedral_angle_4_deg	14.323
r_dihedral_angle_1_deg	6.415
r_scangle_it	6.008
r_scbond_it	4.055
r_mcangle_it	2.252
r_angle_refined_deg	1.304
r_mcbond_it	1.285
r_chiral_restr	0.1
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	71547
Nucleic Acid Atoms
Solvent Atoms	1383
Heterogen Atoms	12

Software

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