3RZ6 | pdb_00003rz6

Neutron structure of perdeuterated rubredoxin using 40 hours 1st pass data

NEUTRON DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.92	α = 90
b = 34.928	β = 90
c = 43.532	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	neutron	293	IMAGE PLATE	MAATEL QLD: LADI-III		2008-05-07	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.3 - 4.2	ILL	LADI III

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	1.65	27.243	74.1	0.117		3.3	4783	4781		2

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	1.65	1.74	30.5		0.164	2.9	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
NEUTRON DIFFRACTION	FOURIER SYNTHESIS	PDB ENTRY 3KYW	1.75	21.766	1.56	4416	201	79.6	0.2092	0.2078	0.2381

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]
-0.3484			1.1494		2.7302

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.802
f_angle_d	1.234
f_chiral_restr	0.067
f_bond_d	0.016
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	394
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	1

Software

Software
Software Name	Purpose
LAUEGEN	data collection
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling