6G59

Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.1M Hepes pH7, 2M NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.924	α = 90
b = 106.855	β = 90
c = 131.023	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS3 2M		2012-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.45	49.5	100	0.2	0.98	6.6	5		44955			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.54	99		1	0.5	1.4	4.9

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	4A3Q	2.45	49.5	42708	2247	99.81	0.1937	0.19259	0.21489	RANDOM	35.447

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]
-1.59			1.2		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.743
r_dihedral_angle_4_deg	15.776
r_dihedral_angle_3_deg	13.79
r_dihedral_angle_1_deg	6.49
r_long_range_B_refined	6.031
r_long_range_B_other	6.022
r_scangle_other	3.32
r_mcangle_other	2.794
r_mcangle_it	2.792
r_scbond_it	2.262
r_scbond_other	2.023
r_mcbond_it	1.669
r_mcbond_other	1.662
r_angle_refined_deg	1.362
r_angle_other_deg	0.939
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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	6068
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
Coot	model building