4LMI | pdb_00004lmi

Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	0.2 M di-Ammonium hydrogen Citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.536	α = 90
b = 69.873	β = 90
c = 94.809	γ = 90

Symmetry
Space Group	P 21 21 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 315r		2012-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

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	1.8	50	98.6	0.067	35.7	7.2	30818	30387		-3

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	1.8	1.83	97.8		0.91	1.98	7.2	1453

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	1.8	50	30334	30334	1536	98.38	0.1606	0.1606	0.1579	0.1575	0.2098	0.2098	RANDOM	34.2618

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]
0.08			0.81		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	28.917
r_dihedral_angle_2_deg	28.642
r_sphericity_bonded	16.494
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_3_deg	12.875
r_dihedral_angle_1_deg	5.738
r_rigid_bond_restr	1.944
r_angle_refined_deg	1.085
r_chiral_restr	0.072
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	28.917
r_dihedral_angle_2_deg	28.642
r_sphericity_bonded	16.494
r_dihedral_angle_4_deg	14.394
r_dihedral_angle_3_deg	12.875
r_dihedral_angle_1_deg	5.738
r_rigid_bond_restr	1.944
r_angle_refined_deg	1.085
r_chiral_restr	0.072
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2169
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

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.