7A0D | pdb_00007a0d

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HRT

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), 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.672	α = 90
b = 102.374	β = 90
c = 142.735	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		2019-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9786	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.6	48.18	99.9	0.096	0.096	0.1	0.028	0.999	13.8	13		56998

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	1.6	1.63	98.3		2.37	2.37	2.47	0.693	0.421	1.1	12.5

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	1HRT	1.6	48.18	56953	2797	99.865	0.184	0.1828	0.18	0.2154	0.22	33.055

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]
0.401			-0.722		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.568
r_dihedral_angle_4_deg	20.721
r_dihedral_angle_3_deg	13.733
r_lrange_it	8.481
r_dihedral_angle_1_deg	7.014
r_scangle_it	6.803
r_scbond_it	4.586
r_mcangle_it	4.122
r_mcbond_it	2.904
r_angle_refined_deg	1.814
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.283
r_symmetry_xyhbond_nbd_refined	0.208
r_nbd_refined	0.207
r_chiral_restr	0.136
r_xyhbond_nbd_refined	0.133
r_metal_ion_refined	0.099
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2801
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	29

Software

Software
Software Name	Purpose
DIALS	data processing
Aimless	data scaling
Aimless	data reduction
PHENIX	phasing
Coot	model building
REFMAC	refinement