4Q2H

Crystal structure of probable proline racemase from agrobacterium radiobacter K84, TARGET EFI-506561, with bound carbonate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	15 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.4 M POTASSIUM PHOSPHATE MONOBASIC, 16% PEG8000, 20% GLYCEROL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.43	α = 90
b = 129.47	β = 90
c = 178.703	γ = 90

Symmetry
Space Group	C 2 2 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	RAYONIX MX225HE	MIRRORS	2014-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		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	1.8	50	99.9	0.085	0.085	20.9	7.3		72154		-5	25.997

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	1.8	1.83	100		0.91	0.91	2.3	7.4

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4LB0	1.8	30	69949	2156	99.64	0.14744	0.14656	0.1757	RANDOM	35.503

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]
-0.47			1.83		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.797
r_dihedral_angle_4_deg	18.207
r_dihedral_angle_3_deg	13.115
r_long_range_B_refined	11.51
r_long_range_B_other	11.509
r_scbond_it	11.235
r_scbond_other	11.233
r_scangle_other	10.943
r_dihedral_angle_1_deg	5.968
r_mcbond_it	4.689
r_mcbond_other	4.689
r_mcangle_it	4.678
r_mcangle_other	4.677
r_angle_refined_deg	1.349
r_angle_other_deg	0.74
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5102
Nucleic Acid Atoms
Solvent Atoms	679
Heterogen Atoms	14

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling