3LF5 | pdb_00003lf5

Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EUE	PDB ENTRY 1EUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	277	2M ammonium sulfate, 0.1M Na/K phosphate, 0.2M lithium sulfate, pH 6.2, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.48	α = 90
b = 56.37	β = 100.67
c = 42.56	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210r		2009-11-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.0000	APS	17-BM

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	1.25	30	99	0.058	13.02		48981	48981		-3	17.458

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	1.25	1.28	93.6		0.724	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1EUE	1.25	18.91	48981	48981	2489	99.07	0.148	0.1468	0.15	0.1726	0.17	Random	12.26

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]
0.474		-0.477	-0.655		0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.598
r_dihedral_angle_4_deg	18.649
r_dihedral_angle_3_deg	11.715
r_dihedral_angle_1_deg	5.275
r_scangle_it	4.906
r_scbond_it	3.416
r_scangle_other	2.682
r_mcangle_it	2.486
r_mcbond_it	1.499
r_angle_refined_deg	1.477
r_rigid_bond_restr	1.27
r_mcangle_other	1.109
r_angle_other_deg	0.883
r_scbond_other	0.723
r_mcbond_other	0.405
r_symmetry_vdw_other	0.219
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1387
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	96

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction