2I02 | pdb_00002i02

CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	277	0.2M NaCl, 40.0% PEG-300, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.646	α = 90
b = 103.646	β = 90
c = 109.695	γ = 120

Symmetry
Space Group	P 63 2 2

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	Flat mirror (vertical focusing)	2006-07-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979197,0.918370	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	29.921	100	0.117	0.117	4.8	10.3		32823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	100		0.946	0.946	0.8	10.6	2377

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	29.921	32793	1663	99.99	0.178	0.177	0.19	0.204	0.21	RANDOM	25.749

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]
-0.55	-0.27		-0.55		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.584
r_dihedral_angle_4_deg	13.334
r_dihedral_angle_3_deg	13.209
r_scangle_it	7.245
r_dihedral_angle_1_deg	6.242
r_scbond_it	5.215
r_mcangle_it	3.393
r_mcbond_it	2.36
r_angle_refined_deg	1.496
r_angle_other_deg	0.88
r_mcbond_other	0.568
r_nbd_refined	0.22
r_symmetry_vdw_other	0.22
r_nbd_other	0.199
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.158
r_nbtor_other	0.088
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2262
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	53

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
SHARP	phasing