3PMA

2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.562	α = 90
b = 87.562	β = 90
c = 191.99	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	104	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku Varimax Confocal optics	2004-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.2	27.92	99.8	0.083	13.4	7.87	38833	38745

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	2.2	2.28	100		0.311	6.3	9.03	3775

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MKX	2.2	27.8	38784	36728	1938	99.78	0.20574	0.20373	0.24456	RANDOM	45.187

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]
-0.15			-0.15		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.213
r_dihedral_angle_4_deg	17.337
r_dihedral_angle_3_deg	15.513
r_dihedral_angle_1_deg	5.498
r_scangle_it	3.491
r_scbond_it	2.342
r_mcangle_it	1.344
r_angle_refined_deg	1.244
r_mcbond_it	0.622
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4393
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	138

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling