3KYW | pdb_00003kyw

Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BRF	PDB entry 1BRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop			3.8 M sodium/potassium phosphate, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.238	α = 90
b = 35.096	β = 90
c = 43.858	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
1	1	x-ray	295	CCD	MAR225		2008-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.1	27.4	98.8	8.9	3.7		21725

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 1BRF	1.1	26.99	21692	1107	98.26	0.153	0.152	0.16	0.165	0.18	RANDOM	15.095

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]
-0.11			0.07		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.316
r_dihedral_angle_3_deg	10.509
r_dihedral_angle_1_deg	5.755
r_scangle_it	3.856
r_sphericity_bonded	3.45
r_scbond_it	2.981
r_mcangle_it	2.6
r_mcbond_it	1.84
r_angle_refined_deg	1.508
r_rigid_bond_restr	1.439
r_mcbond_other	1.257
r_sphericity_free	1.221
r_angle_other_deg	0.855
r_symmetry_hbond_refined	0.254
r_nbd_refined	0.211
r_nbtor_refined	0.193
r_nbd_other	0.18
r_symmetry_vdw_other	0.151
r_symmetry_vdw_refined	0.119
r_nbtor_other	0.098
r_chiral_restr	0.096
r_xyhbond_nbd_refined	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	419
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ELVES	data scaling