1WVN

Crystal Structure of domain 3 of human alpha polyC binding protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295HEPES, lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.4α = 90
b = 71β = 90
c = 29.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC mirrors2002-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
12.135.5198.90.04227.4659113817-330.2
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)
2.12.1787.70.2583.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EC62.135.515911381746298.010.2150.2140.190220.24758RANDOM26.124
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]
0.01-0.520.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.717
r_dihedral_angle_4_deg23.5
r_dihedral_angle_3_deg17.088
r_dihedral_angle_1_deg4.948
r_scangle_it3.55
r_scbond_it2.283
r_mcangle_it1.537
r_angle_refined_deg1.279
r_mcbond_it0.954
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.717
r_dihedral_angle_4_deg23.5
r_dihedral_angle_3_deg17.088
r_dihedral_angle_1_deg4.948
r_scangle_it3.55
r_scbond_it2.283
r_mcangle_it1.537
r_angle_refined_deg1.279
r_mcbond_it0.954
r_nbtor_refined0.29
r_xyhbond_nbd_refined0.23
r_nbd_refined0.2
r_symmetry_vdw_refined0.189
r_symmetry_hbond_refined0.183
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms539
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing