3EEZ | pdb_00003eez

Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Silicibacter pomeroyi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QDD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	20% PEG 3350, 200mM lithium nitrate, pH 7.0, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.626	α = 90
b = 110.626	β = 90
c = 120.272	γ = 90

Symmetry
Space Group	P 4 2 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		2008-03-08	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	2.8	30.686	93.3	0.181	0.181	10.9	8.5	18785	17526			60.7

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)
	2.8	2.95	94.9		0.568	0.568	2.8	8.5	2556

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	2QDD	2.8	20	18747	17478	905	93.23	0.231	0.228	0.231	0.279	0.2758	RANDOM	53.382

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]
-5.11			-5.11		10.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.471
r_dihedral_angle_3_deg	22.121
r_dihedral_angle_4_deg	20.493
r_dihedral_angle_1_deg	6.505
r_scangle_it	2.405
r_angle_refined_deg	1.574
r_scbond_it	1.474
r_mcangle_it	1.174
r_mcbond_it	0.705
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.241
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2748
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
MOLREP	phasing