2PZV | pdb_00002pzv

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	1.4 M ammonium sulphate, 7% (v/v) 2-propanol, 40 mM potasium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.905	α = 90.02
b = 50.54	β = 89.98
c = 72.29	γ = 110.21

Symmetry
Space Group	P 1

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 315		2004-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	1.25	50	93	0.037		2.2	119468	111105

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)
	1.25	1.29			0.415		1.8

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	1.25	22.54	110554	11094	86.04	0.188	0.183	0.19	0.227	0.18	RANDOM	26.57

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]
0.45	-0.03	0.11	-0.19	0.09	-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.164
r_dihedral_angle_4_deg	21.672
r_dihedral_angle_3_deg	15.453
r_sphericity_free	12.446
r_sphericity_bonded	8.542
r_scangle_it	6.712
r_dihedral_angle_1_deg	6.157
r_scbond_it	4.901
r_mcangle_it	3.948
r_rigid_bond_restr	3.21
r_mcbond_it	2.859
r_angle_refined_deg	2.024
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.272
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.19
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.139
r_bond_refined_d	0.021
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing