3E6P | pdb_00003e6p

Crystal structure of human meizothrombin desF1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A0H	PDB entries 1A0H, 1SHH
experimental model	PDB	1SHH	PDB entries 1A0H, 1SHH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	295	0.2M Na2(SO4), 23% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.336	α = 90
b = 121.336	β = 90
c = 100.204	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	ADSC QUANTUM 315		2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90000	APS	14-BM-C

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	2.1	40	92.4	0.112	17.7	11.8	43798	40469		-0.5

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	2.1	2.18	79		0.438	2	5.2	3398

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 (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	THROUGHOUT	PDB entries 1A0H, 1SHH	2.1	32.58	38428	38428	2026	92.18	0.21304	0.21304	0.21109	0.2087	0.24946	0.2441	RANDOM	44.5

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.918
r_dihedral_angle_4_deg	19.575
r_dihedral_angle_3_deg	19.53
r_dihedral_angle_1_deg	6.988
r_scangle_it	4.284
r_scbond_it	2.741
r_mcangle_it	1.938
r_angle_refined_deg	1.741
r_mcbond_it	1.021
r_chiral_restr	0.125
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3203
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing