8JU4 | pdb_00008ju4

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

X-RAY DIFFRACTION

---

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	6.5	289.15	0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph 6.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
4.43	72.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.89	α = 90
b = 118.89	β = 90
c = 118.61	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	2.3	29.705	99.9	0.107	19.2	20.6		42707

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	2.3	2.36			1.584

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	2.3	29.705	42673	2164	99.92	0.193	0.1917	0.2	0.2229	0.23	53.403

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]
1.172	0.586		1.172		-3.802

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.846
r_dihedral_angle_4_deg	21.129
r_dihedral_angle_3_deg	16.741
r_lrange_it	13.369
r_lrange_other	13.368
r_scangle_it	9.034
r_scangle_other	9.033
r_dihedral_angle_1_deg	6.874
r_scbond_it	6.623
r_scbond_other	6.622
r_mcangle_it	5.975
r_mcangle_other	5.974
r_mcbond_it	4.688
r_mcbond_other	4.669
r_angle_other_deg	2.459
r_angle_refined_deg	1.716
r_symmetry_nbd_refined	0.35
r_nbd_other	0.332
r_symmetry_nbd_other	0.227
r_nbd_refined	0.21
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.075
r_bond_other_d	0.037
r_symmetry_xyhbond_nbd_refined	0.035
r_gen_planes_other	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3842
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-2000	data reduction
PHASER	phasing