2GGE | pdb_00002gge

Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme from Bacillus Subtilis complexed with MG++ at 1.8 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	100mM Bis-Tris, pH 5.5, 15% PEG 3350, 200mM Magnesium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.417	α = 90
b = 110.654	β = 105.77
c = 129.308	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm	SGX-CAT	2006-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	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	1.884	27.948	86.8	0.127	0.127	5	3.2	245740	213305			25.7

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)
	1.88	1.98	69.6	69.6	0.016	0.01645	0.4	2.8	24866

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 (All)	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	1MUC	1.89	27.95	245740	209379	10531	85.7	0.192	0.192	0.189	0.19	0.253	0.25	RANDOM	25.791

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]
		-0.01	-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.305
r_dihedral_angle_4_deg	20.182
r_dihedral_angle_3_deg	16.378
r_dihedral_angle_1_deg	6.515
r_scangle_it	4.701
r_scbond_it	3.147
r_mcangle_it	1.919
r_angle_refined_deg	1.87
r_mcbond_it	1.288
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.305
r_dihedral_angle_4_deg	20.182
r_dihedral_angle_3_deg	16.378
r_dihedral_angle_1_deg	6.515
r_scangle_it	4.701
r_scbond_it	3.147
r_mcangle_it	1.919
r_angle_refined_deg	1.87
r_mcbond_it	1.288
r_nbtor_refined	0.315
r_xyhbond_nbd_refined	0.312
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.208
r_chiral_restr	0.127
r_metal_ion_refined	0.064
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23911
Nucleic Acid Atoms
Solvent Atoms	1710
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
CCP4	data scaling

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.