6ZV8 | pdb_00006zv8

Crystal Structure of Thrombin in complex with compound51

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		INHOUSE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		283	0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.166	α = 90
b = 70.342	β = 100.28
c = 71.372	γ = 90

Symmetry
Space Group	C 1 2 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	Nonius Kappa CCD	MIRRORS	2012-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54187

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	1.59	70.23	89.2	0.06	12.95	2.84		130734		2

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	1.59	1.61	89		0.279		1.96

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	INHOUSE	1.7	70.22	31333	1618	88.88	0.2052	0.203	0.21	0.2473	0.25	RANDOM	18.885

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]
0.57		-0.38	-0.45		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES, PERIOD 2 (DEGREES)	33.059
TORSION ANGLES, PERIOD 3 (DEGREES)	14.353
TORSION ANGLES, PERIOD 4 (DEGREES)	12.948
TORSION ANGLES, PERIOD 1 (DEGREES)	6.86
BOND ANGLES REFINED (DEGREES)	2.212
BOND ANGLES OTHERS (DEGREES)	0.915
CHIRAL-CENTER RESTRAINTS (A**3)	0.121
BOND LENGTHS REFINED (A)	0.023
GENERAL PLANES REFINED (A)	0.012
BOND LENGTHS OTHERS (A)	0.002
GENERAL PLANES OTHERS (A)	0.001
NON-BONDED CONTACTS REFINED (A)
NON-BONDED CONTACTS OTHERS (A)
NON-BONDED TORSION REFINED (A)
NON-BONDED TORSION OTHERS (A)
H-BOND (X...Y) REFINED (A)
SYMMETRY VDW REFINED (A)
SYMMETRY VDW OTHERS (A)
SYMMETRY H-BOND REFINED (A)

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2342
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	14

Software

Software
Software Name	Purpose
SAINT	data reduction
XPREP	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction