3DAX | pdb_00003dax

Crystal structure of human CYP7A1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IAG	pdb entry 2iag

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	20% PEG400, 0.1M potassium chloride, 0.1M trisodium citrate, pH 5.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3	58.3
3	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.339	α = 64.36
b = 80.159	β = 75.23
c = 84.937	γ = 72.17

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315		2007-09-21	M	SINGLE WAVELENGTH
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.96860	NSLS	X25
2

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
1,2	2.1	40	92	0.063	11.1	3.7		65596

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)
	2.1	2.18	68.2		0.402		3.1	4818

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	mr, MR	THROUGHOUT	pdb entry 2iag	2.15	30	63038	2018	93.449	0.19	0.189	0.1922	0.228	0.2289	thin shells (sftools)	31.625

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]
-0.061	-0.162	-0.007	0.081	0.19	-0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.131
r_dihedral_angle_4_deg	18.185
r_dihedral_angle_3_deg	14.595
r_dihedral_angle_1_deg	5.969
r_mcangle_it	3.606
r_scangle_it	3.393
r_mcbond_it	2.526
r_scbond_it	2.432
r_angle_refined_deg	1.288
r_angle_other_deg	0.877
r_mcbond_other	0.615
r_symmetry_hbond_refined	0.217
r_symmetry_vdw_other	0.205
r_nbd_refined	0.202
r_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.122
r_symmetry_vdw_refined	0.098
r_nbtor_other	0.086
r_chiral_restr	0.079
r_bond_refined_d	0.017
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7519
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	88

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
MolProbity	model building