3LZW | pdb_00003lzw

Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZBW	PDB ENTRY 2ZBW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M HEPES buffer (pH 7.5), 30% 1,2-propanediol, 20% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.9	α = 90
b = 135.724	β = 90
c = 39.191	γ = 90

Symmetry
Space Group	P 21 21 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	RIGAKU JUPITER 210		2008-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	26.87	99.9	0.071		7		32363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	99.5		0.388		6.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZBW	1.8	26.87	30707	1602	100	0.17023	0.16885	0.17	0.19645	0.2	RANDOM	24.212

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]
0.17			-0.71		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.807
r_dihedral_angle_3_deg	12.417
r_dihedral_angle_4_deg	8.977
r_dihedral_angle_1_deg	5.3
r_scangle_it	1.976
r_angle_refined_deg	1.253
r_scbond_it	1.237
r_angle_other_deg	0.799
r_mcangle_it	0.796
r_mcbond_it	0.422
r_symmetry_vdw_other	0.231
r_nbd_refined	0.195
r_nbd_other	0.176
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.133
r_symmetry_hbond_refined	0.131
r_symmetry_vdw_refined	0.117
r_metal_ion_refined	0.107
r_mcbond_other	0.091
r_nbtor_other	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2570
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	103

Software

Software
Software Name	Purpose
BSS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling