4FS9 | pdb_00004fs9

Complex structure of a broad specificity amino acid racemase (Bar) within the reactive intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DYJ	PDB ENTRY 4DYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.1M bicine (pH9.0), 0.1M NaCl, 20% PEG-MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.418	α = 90
b = 118.109	β = 99.87
c = 74.024	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 210r		2012-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.00	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	20	98.1			22074	21656		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.21	98.4

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	PDB ENTRY 4DYJ	3.1	20	20809	20576	1072	98.88	0.17694	0.17479	0.1819	0.21892	0.1902	RANDOM	43.224

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]
-4.55		-3.91	-7.22		10.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.156
r_dihedral_angle_3_deg	23.182
r_dihedral_angle_4_deg	21.726
r_dihedral_angle_1_deg	7.819
r_mcangle_it	1.762
r_scangle_it	1.647
r_angle_refined_deg	1.376
r_mcbond_it	1.018
r_scbond_it	1.004
r_chiral_restr	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5840
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	50

Software

Software
Software Name	Purpose
SPEC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling