Experiment: 3GIS

Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JOU	PDB ENTRY 1JOU, 1DX5
experimental model	PDB	1DX5	PDB ENTRY 1JOU, 1DX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.25	α = 90
b = 100.34	β = 90
c = 229.28	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	ADSC QUANTUM 4	mirrors	2007-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.979	SRS	PX14.2

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	2.4	91.9	96	0.15	8.9	4.7	60765	58334

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	2.4	2.53	95		0.339	3.5	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1JOU, 1DX5	2.4	40	2	60715	57399	2875	94.5	0.247	0.243	0.211	0.2154	0.259	0.2152	RANDOM	28.213

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]
4.64			-6.867		2.227

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.956
c_mcangle_it	2.173
c_scbond_it	1.999
c_angle_d	1.347
c_mcbond_it	1.317
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9539
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	78

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection