4QDD | pdb_00004qdd

Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with 1,4-30Q-CoA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	294	0.5 M NaH2PO4, 0.125 M K2HPO4, 4% PEG-1000, 20 mM Tris, 0.1 mM phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.17	α = 90
b = 163.17	β = 90
c = 47.14	γ = 120

Symmetry
Space Group	P 63

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	RAYONIX MX300HE	mirrors	2012-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.98	CLSI	08B1-1

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	2.6	141.309	100	0.244	7.1	6.7	22485	22485

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	2.6	2.74	100		0.013	1.278	0.6	6.2	3248

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 (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	2.6	53.41	22477	1117	99.97	0.2265	0.2249	0.22	0.256	0.25	RANDOM	50.678

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]
18.07			18.07		-36.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.756
r_dihedral_angle_3_deg	15.095
r_dihedral_angle_4_deg	9.996
r_dihedral_angle_1_deg	6.173
r_mcangle_it	3.99
r_angle_other_deg	3.643
r_mcbond_it	2.629
r_mcbond_other	2.617
r_angle_refined_deg	0.966
r_chiral_restr	0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.756
r_dihedral_angle_3_deg	15.095
r_dihedral_angle_4_deg	9.996
r_dihedral_angle_1_deg	6.173
r_mcangle_it	3.99
r_angle_other_deg	3.643
r_mcbond_it	2.629
r_mcbond_other	2.617
r_angle_refined_deg	0.966
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_other	0.005
r_gen_planes_refined	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2959
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	37

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.