5WXX | pdb_00005wxx

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	25% (w/v) polyethylene glycol 3350, 0.1 M sodium citrate, pH 6.5, 0.2 magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.751	α = 90
b = 128.751	β = 90
c = 46.182	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		2011-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97930	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	2.35	111.5	99.9	32.4	12.7		18567

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	2.35	2.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	2.35	42.667	17611	940	99.86	0.18732	0.18651	0.19	0.20217	0.2	RANDOM	48.978

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]
-1.23	-0.62		-1.23		4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.802
r_dihedral_angle_4_deg	20.039
r_dihedral_angle_3_deg	14.853
r_dihedral_angle_1_deg	6.093
r_long_range_B_refined	5.642
r_long_range_B_other	5.641
r_scangle_other	4.22
r_mcangle_it	2.811
r_mcangle_other	2.811
r_scbond_other	2.471
r_scbond_it	2.468
r_mcbond_it	1.721
r_mcbond_other	1.719
r_angle_refined_deg	1.165
r_angle_other_deg	0.879
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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	79
Heterogen Atoms	13

Software

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