2I51 | pdb_00002i51

CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-related, FMN binding protein (NPUN_F5749) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.40 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			277	20.0% Glycerol, 24.0% PEG-1500, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.647	α = 90
b = 65.928	β = 90
c = 112.38	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
2	1	x-ray		CCD	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-07-02	M	MAD
1	1		CCD	ADSC QUANTUM 315	1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing	2006-07-07

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.978489	SSRL	BL1-5
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979264,0.911617	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
2	1.397	29.386	99.7	0.113	0.113	3.5	5.2		96246			15.91

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)
2	1.4	1.44	98		0.01	0.01016	0.7	4.6	6910

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	MAD	THROUGHOUT	1.4	29.386	96170	4853	99.59	0.166	0.165	0.1744	0.188	0.1974	RANDOM	16.71

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]
-0.01			0.45		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.686
r_dihedral_angle_4_deg	15.905
r_dihedral_angle_3_deg	12.16
r_scangle_it	6.091
r_dihedral_angle_1_deg	5.541
r_scbond_it	4.321
r_mcangle_it	3.065
r_mcbond_it	2.135
r_angle_refined_deg	1.637
r_angle_other_deg	0.974
r_mcbond_other	0.506
r_symmetry_vdw_other	0.331
r_symmetry_vdw_refined	0.31
r_nbd_other	0.227
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.107
r_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3120
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	148

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
autoSHARP	phasing