3KW3 | pdb_00003kw3

Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DY3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, 25% PEG 3350 and soaked for 1 hour in 0.1 M Hepes pH 8.0, 1.0 M KI, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.794	α = 90
b = 54.316	β = 112.39
c = 107.476	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	100	CCD	ADSC QUANTUM 315		2009-07-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2009-11-16	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.04	50	99.5	0.088	17.4	5.3		45971

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	2.04	2.12	96.7		0.496	2.79	4.6	4405

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD, MR	THROUGHOUT	2DY3	2.04	34.9	45875	2318	98.54	0.193	0.191	0.19	0.233	0.24	RANDOM	22.817

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]
-0.82		-1.88	-1.01		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.335
r_dihedral_angle_4_deg	16.392
r_dihedral_angle_3_deg	15.135
r_dihedral_angle_1_deg	6.391
r_scangle_it	3.061
r_scbond_it	1.954
r_angle_refined_deg	1.408
r_mcangle_it	1.167
r_mcbond_it	0.664
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.335
r_dihedral_angle_4_deg	16.392
r_dihedral_angle_3_deg	15.135
r_dihedral_angle_1_deg	6.391
r_scangle_it	3.061
r_scbond_it	1.954
r_angle_refined_deg	1.408
r_mcangle_it	1.167
r_mcbond_it	0.664
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5407
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

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.