7A0E | pdb_00007a0e

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7A0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	297	38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), and 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.099	α = 90
b = 101.995	β = 90
c = 144.044	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2020-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.9	72.02	98.05	0.206	0.206	0.216	0.062	0.992	5	10.6		33481

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93			1.848	1.848	2.148	1.061	0.873	0.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7A0D	1.9	72.02	33424	1572	97.894	0.216	0.2139	0.21	0.2629	0.26	40.955

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]
0.548			-0.38		-0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.672
r_dihedral_angle_4_deg	19.236
r_dihedral_angle_3_deg	16.33
r_lrange_it	8.384
r_dihedral_angle_1_deg	7.362
r_scangle_it	5.734
r_mcangle_it	4.208
r_scbond_it	3.906
r_mcbond_it	2.78
r_angle_refined_deg	1.453

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.672
r_dihedral_angle_4_deg	19.236
r_dihedral_angle_3_deg	16.33
r_lrange_it	8.384
r_dihedral_angle_1_deg	7.362
r_scangle_it	5.734
r_mcangle_it	4.208
r_scbond_it	3.906
r_mcbond_it	2.78
r_angle_refined_deg	1.453
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.274
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.108
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2852
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	15

Software

Software
Software Name	Purpose
xia2	data processing
xia2	data reduction
xia2	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

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.