1BVK

HUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VFBHULYS STRUCTURE, AND LYSOZYME FROM PDB ENTRY 1VFB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6753.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.7α = 90
b = 97.7β = 90
c = 174.9γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATERIGAKUR-AXIS IIC1996-11-22M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.75093.20.0750.0759.65.42237944.1
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)RedundancyNumber Unique Reflections (All)
2.72.7573.50.4520.452

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHULYS STRUCTURE, AND LYSOZYME FROM PDB ENTRY 1VFB2.710218822189580.30.2080.2080.297RANDOM31.1
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
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.3
x_mcangle_it11.7
x_scangle_it11.7
x_mcbond_it9.91
x_scbond_it9.91
x_angle_deg1.8
x_improper_angle_d1.7
x_bond_d0.014
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.3
x_mcangle_it11.7
x_scangle_it11.7
x_mcbond_it9.91
x_scbond_it9.91
x_angle_deg1.8
x_improper_angle_d1.7
x_bond_d0.014
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5490
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing