5WXZ

Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with D-aspartate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WXX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	25% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.097	α = 90
b = 129.097	β = 90
c = 44.641	γ = 120

Symmetry
Space Group	P 32 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 315r		2011-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97915	SSRF	BL17U

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	2.8	111.8	99.9	15.2	4.8		10736

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	2.8	2.85

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	5WXX	2.8	42.257	10225	503	99.9	0.18421	0.18326	0.20246	RANDOM	60.504

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]
-0.59	-0.3		-0.59		1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.22
r_dihedral_angle_3_deg	15.127
r_dihedral_angle_4_deg	12.988
r_long_range_B_refined	7.609
r_long_range_B_other	7.607
r_dihedral_angle_1_deg	6.663
r_scangle_other	5.229
r_mcangle_it	4.516
r_mcangle_other	4.514
r_scbond_it	3.117
r_scbond_other	3.116
r_mcbond_it	2.754
r_mcbond_other	2.751
r_angle_refined_deg	1.264
r_angle_other_deg	0.895
r_chiral_restr	0.069
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	1786
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	9

Software

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