5DR5

Crystal structure of the sclerostin-neutralizing Fab AbD09097


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NH7PDB entry 3NH7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529420% (w/v) PEG3350, 0.1M HEPES pH 7.5, 10mM zinc chloride
Crystal Properties
Matthews coefficientSolvent content
2.0840.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.193α = 90
b = 78.495β = 95.71
c = 59.196γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCRigaku VariMax HF2012-06-13MSINGLE 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
11.8520.7797.90.06810.53.663514634389
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)
11.851.9280.10.33.72.942803

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3NH71.8520.7732559172197.490.19130.18840.2442RANDOM29.759
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]
0.88-1.18-0.23-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_4_deg23.529
r_dihedral_angle_3_deg16.049
r_dihedral_angle_1_deg7.563
r_mcangle_it2.517
r_scbond_it2.291
r_angle_refined_deg2.006
r_mcbond_it1.7
r_chiral_restr0.133
r_bond_refined_d0.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_4_deg23.529
r_dihedral_angle_3_deg16.049
r_dihedral_angle_1_deg7.563
r_mcangle_it2.517
r_scbond_it2.291
r_angle_refined_deg2.006
r_mcbond_it1.7
r_chiral_restr0.133
r_bond_refined_d0.018
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3346
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction