2GDE | pdb_00002gde

Thrombin in complex with inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	PEG, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.084	α = 90
b = 72.169	β = 99.06
c = 70.357	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2005-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.54179

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	69.5	98	0.103	0.103	3.7	3.3		22924

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)
1	2	2.11	96.3	96.3	0.363	0.363	2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	69.5	22924	22924	924	97.67	0.211	0.211	0.209	0.248	RANDOM	47.359

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]
0.92		-2.63	-2.23		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.807
r_dihedral_angle_3_deg	17.132
r_dihedral_angle_4_deg	14.581
r_dihedral_angle_1_deg	6.662
r_scangle_it	3.348
r_scbond_it	2.123
r_angle_refined_deg	1.577
r_mcangle_it	1.567
r_mcbond_it	0.859
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.249
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	45

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CCP4	data scaling
MOLREP	phasing