7A0F | pdb_00007a0f

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution

X-RAY DIFFRACTION

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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), 0.3 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.069	α = 90
b = 101.498	β = 90
c = 142.075	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 PILATUS 6M		2019-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.9778	PETRA III, DESY	P11

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	2.7	47.79	100	0.287	0.287	0.299	0.082	0.992	8.9	13.1		11928

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	2.7	2.83			1.8	1.8	1.873	0.514	0.592	1.6

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	2.7	47.79	11902	586	99.933	0.196	0.1936	0.19	0.2532	0.25	45.168

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]
-0.848			0.639		0.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.42
r_dihedral_angle_4_deg	20.966
r_dihedral_angle_3_deg	17.975
r_lrange_it	10.929
r_dihedral_angle_1_deg	10.113
r_scangle_it	6.841
r_mcangle_it	5.638
r_scbond_it	4.378
r_mcbond_it	3.456
r_angle_refined_deg	1.744
r_nbtor_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.286
r_ext_dist_refined_d	0.278
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.147
r_metal_ion_refined	0.141
r_chiral_restr	0.126
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2848
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	15

Software

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