3LZX | pdb_00003lzx

Crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (FORM II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LZW	PDB ENTRY 3LZW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	20% PEG 3350, 0.2M Sodium fluoride, 5% Trehalose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.466	α = 90
b = 64.85	β = 105.82
c = 61.116	γ = 90

Symmetry
Space Group	C 1 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	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	1.9	26.85	96.9	0.051		3.6		59771

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)
	1.9	1.97	80.4		0.22		3

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 3LZW	1.9	26.85	56728	3014	100	0.18267	0.18113	0.19	0.2111	0.22	RANDOM	26.974

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]
-1.37		-0.99	-0.31		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.38
r_dihedral_angle_4_deg	15.436
r_dihedral_angle_3_deg	12.673
r_dihedral_angle_1_deg	5.608
r_scangle_it	2.423
r_scbond_it	1.505
r_angle_refined_deg	1.325
r_mcangle_it	0.965
r_angle_other_deg	0.81
r_mcbond_it	0.513
r_symmetry_vdw_other	0.219
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.189
r_nbd_other	0.182
r_nbtor_refined	0.174
r_metal_ion_refined	0.144
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.129
r_mcbond_other	0.107
r_nbtor_other	0.081
r_symmetry_vdw_refined	0.067
r_bond_refined_d	0.009
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	5140
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	204

Software

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