Experiment: 2H9T

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	100 mM tris, 25 % tert-butanol, 0.16 mM thrombin:suramin complex, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.966	α = 90
b = 76.202	β = 90
c = 113.848	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARRESEARCH		2005-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.438	LNLS	D03B-MX1

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	2.4	41.03	100	0.18	0.18	4.1	4.9		15625			27.82

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)
	2.4	2.53	100		0.549	0.549	3.1	4.9	2233

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PPB	2.4	41.03	3.1	14978	15579	781	99.98	0.184	0.184	0.18	0.266	RANDOM	28.664

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.293
r_dihedral_angle_3_deg	20.01
r_dihedral_angle_4_deg	19.907
r_dihedral_angle_1_deg	7.76
r_scangle_it	3.524
r_scbond_it	2.318
r_angle_refined_deg	2.059
r_mcangle_it	1.407
r_mcbond_it	0.812
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.293
r_dihedral_angle_3_deg	20.01
r_dihedral_angle_4_deg	19.907
r_dihedral_angle_1_deg	7.76
r_scangle_it	3.524
r_scbond_it	2.318
r_angle_refined_deg	2.059
r_mcangle_it	1.407
r_mcbond_it	0.812
r_nbtor_refined	0.326
r_nbd_refined	0.269
r_symmetry_hbond_refined	0.265
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.14
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2282
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	86

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.