3NHX | pdb_00003nhx

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M8C	PDB ENTRY 3M8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	298	2 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.28	α = 90
b = 61.28	β = 90
c = 142.861	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	MARMOSAIC 325 mm CCD		2010-03-25		SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-03-24		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.59	28.572	100	0.072	19.9	13.7		22234			21.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.59	1.68	100		0.744	0.744	1	14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 ENTRY 3M8C	1.59	28.57	22163	22163	1133	100	0.185	0.183	0.18	0.219	0.22	RANDOM	24.05

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]
0.51	0.26		0.51		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.436
r_dihedral_angle_4_deg	20.608
r_dihedral_angle_3_deg	13.493
r_dihedral_angle_1_deg	6.392
r_scangle_it	5.548
r_scbond_it	3.832
r_angle_refined_deg	2.615
r_mcangle_it	2.394
r_mcbond_it	1.548
r_chiral_restr	0.205
r_bond_refined_d	0.032
r_gen_planes_refined	0.017
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	945
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	71

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction