3IK4

CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		150MM POTASSIUM BROMIDE, PH 7.5, 30% PEG2000 MME, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.026	α = 90
b = 93.344	β = 112.6
c = 85.914	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	90	CCD	ADSC QUANTUM 315	MIRRORS	2009-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.07	50	98.9	0.063	7.9	4.1		75228		-5	43.053

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	2.07	2.14	91.2		0.78	0.9	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	1JPM	2.1	20	68809	2147	99.37	0.21855	0.21676	0.27531	RANDOM	41.917

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]
-2.51		-1.49	-1.73		3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.668
r_dihedral_angle_4_deg	19.369
r_dihedral_angle_3_deg	18.049
r_scangle_it	12.844
r_scbond_it	10.315
r_mcangle_it	7.058
r_dihedral_angle_1_deg	5.467
r_mcbond_it	5.364
r_angle_refined_deg	1.253
r_nbtor_refined	0.291
r_xyhbond_nbd_refined	0.159
r_nbd_refined	0.146
r_symmetry_hbond_refined	0.138
r_symmetry_vdw_refined	0.119
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10201
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	16

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling