4O03

Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NZQPDB entry 4NZQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100 mM HEPES, pH 7.5, 10% PEG 4000 and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.9275.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.459α = 90
b = 89.431β = 116.36
c = 87.982γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.384095.80.1286.92.91736416635-0.7-0.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.383.4692.40.4322.1805

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4NZQ3.3839.75-0.7-0.7166381575383594.680.235390.232990.27942RANDOM73.096
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]
0.22-0.05-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.199
r_dihedral_angle_3_deg23.777
r_dihedral_angle_4_deg20.261
r_dihedral_angle_1_deg8.397
r_scangle_it2.04
r_angle_refined_deg1.65
r_mcangle_it1.196
r_scbond_it1.148
r_mcbond_it0.639
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.199
r_dihedral_angle_3_deg23.777
r_dihedral_angle_4_deg20.261
r_dihedral_angle_1_deg8.397
r_scangle_it2.04
r_angle_refined_deg1.65
r_mcangle_it1.196
r_scbond_it1.148
r_mcbond_it0.639
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4321
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms47

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling