8JOJ | pdb_00008joj

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate

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		291	UPH2O,3.5M Sodium formate pH7.0

Crystal Properties
Matthews coefficient	Solvent content
4.43	72.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.603	α = 90
b = 119.603	β = 90
c = 117.304	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)	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	2.819	103.58	95.7	0.165	17.2	20.5		22365

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	2.82	2.97			1.341

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	2.819	77.764	22337	1135	95.703	0.191	0.1887	0.19	0.2345	0.23	64.51

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]
1.793	0.897		1.793		-5.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.177
r_dihedral_angle_4_deg	22.745
r_dihedral_angle_3_deg	18.07
r_lrange_other	11.302
r_lrange_it	11.296
r_scangle_it	8.742
r_scangle_other	8.74
r_mcangle_other	6.683
r_mcangle_it	6.682
r_dihedral_angle_1_deg	6.434
r_scbond_it	6.046
r_scbond_other	6.044
r_mcbond_it	4.72
r_mcbond_other	4.711
r_angle_other_deg	2.43
r_angle_refined_deg	1.557
r_nbd_other	0.259
r_symmetry_nbd_refined	0.257
r_symmetry_nbd_other	0.233
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.066
r_bond_other_d	0.037
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3842
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	83

Software

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