3DL9 | pdb_00003dl9

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CZH	PDB entry 3CZH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	291	1.2M Ammounium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.303	α = 90
b = 163.04	β = 90
c = 152.588	γ = 90

Symmetry
Space Group	C 2 2 21

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 315		2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	2.72	50	99.9	0.163	8	7.2		46055

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)
	2.72	2.77	100		0.957		7.2	2276

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3CZH	2.721	30	45761	1369	99.213	0.184	0.183	0.19	0.218	0.22	thin shells (sftools)	37.005

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]
3.837			-2.163		-1.675

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.272
r_dihedral_angle_4_deg	22.841
r_dihedral_angle_3_deg	14.219
r_dihedral_angle_1_deg	5.462
r_mcangle_it	2.171
r_scangle_it	1.555
r_angle_refined_deg	1.392
r_mcbond_it	1.331
r_scbond_it	1.035
r_angle_other_deg	1.019
r_symmetry_vdw_other	0.284
r_nbd_refined	0.211
r_mcbond_other	0.198
r_nbtor_refined	0.186
r_nbd_other	0.185
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.092
r_nbtor_other	0.088
r_symmetry_hbond_refined	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7453
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	386

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
REFMAC	phasing