2PKS | pdb_00002pks

Thrombin in complex with inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	27% PEG8000, 0.1M SODIUM PHOSPHATE, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.3
2.7	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.942	α = 90
b = 71.843	β = 100.23
c = 70.778	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	MARRESEARCH			M	SINGLE WAVELENGTH
2	1	x-ray		M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	69.673	91.1	0.086	0.086	6.7	2.3	25416	10962	1	1

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	2.5	2.57	93.9		0.526	0.423	1.8	2.2	823

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 (All)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	69.67	10553	502	87.69	0.188	0.185	0.259	RANDOM	41.912

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]
0.2		-2.72	-2.35		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_3_deg	19.153
r_dihedral_angle_4_deg	16.851
r_dihedral_angle_1_deg	7.528
r_scangle_it	4.046
r_scbond_it	2.528
r_angle_refined_deg	1.915
r_mcangle_it	1.894
r_mcbond_it	1.017
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_3_deg	19.153
r_dihedral_angle_4_deg	16.851
r_dihedral_angle_1_deg	7.528
r_scangle_it	4.046
r_scbond_it	2.528
r_angle_refined_deg	1.915
r_mcangle_it	1.894
r_mcbond_it	1.017
r_nbtor_refined	0.315
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.244
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2327
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	27

Software

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

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.