8JBZ | pdb_00008jbz

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 4-androstadiene-3,17- dione

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	1.8 M Ammonium citrate tribasic, pH7.0

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.108	α = 90
b = 120.108	β = 90
c = 117.242	γ = 120

Symmetry
Space Group	P 31 1 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.079	104.234	100	1	16.2	10.5		58119

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.14			0.858

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.079	104.234	58114	2850	99.923	0.196	0.1944	0.2	0.2286	0.24	41.679

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]
0.813	0.407		0.813		-2.637

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.662
r_dihedral_angle_4_deg	21.173
r_dihedral_angle_3_deg	15.645
r_lrange_other	7.884
r_lrange_it	7.878
r_scangle_it	7.735
r_scangle_other	7.733
r_dihedral_angle_1_deg	6.626
r_scbond_it	5.801
r_scbond_other	5.8
r_mcangle_it	4.728
r_mcangle_other	4.727
r_mcbond_it	3.665
r_mcbond_other	3.665
r_angle_other_deg	2.442
r_angle_refined_deg	1.762
r_nbd_other	0.409
r_symmetry_nbd_refined	0.391
r_symmetry_nbd_other	0.218
r_nbd_refined	0.214
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.037
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3812
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing