4AT0 | pdb_00004at0

The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D4C	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY
experimental model	PDB	1E39	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY
experimental model	PDB	1KF6	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY
experimental model	PDB	1NEK	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY
experimental model	PDB	1ZOY	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.233	α = 90
b = 114.308	β = 90
c = 110.161	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 210r	MIRRORS	2007-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16		ESRF	BM16

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	1.6	49.6	97	0.08	22.6	11.1		80282			16

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	1.6	1.69	83.8		0.32	4.7	6.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY	1.6	39.65	75998	4019	96.94	0.15875	0.15786	0.16	0.17539	0.17	RANDOM	16.802

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]
-0.02					0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.61
r_dihedral_angle_4_deg	15.35
r_dihedral_angle_3_deg	11.26
r_dihedral_angle_1_deg	5.367
r_angle_refined_deg	1.436
r_angle_other_deg	0.869
r_nbtor_refined	0.307
r_nbd_other	0.3
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.225
r_nbtor_other	0.142
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.102
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3598
Nucleic Acid Atoms
Solvent Atoms	608
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing