4NWT

Crystal structure of the anti-human NGF Fab APE1531


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QOTPDB ENTRY 3QOT for VHVL, 3SOB for CH1CL
experimental modelPDB 3SOBPDB ENTRY 3QOT for VHVL, 3SOB for CH1CL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529512% PEG 20000, 0.1M NaCl, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5251.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.72α = 90
b = 64.36β = 108.67
c = 63.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 6M2012-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97830SSRLBL11-1

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
11.7538.6498.50.04825.36.948714
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)
11.751.897.70.6042.96.6

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 3QOT for VHVL, 3SOB for CH1CL1.7538.6446262245298.280.151940.15040.18121RANDOM29.289
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]
0.140.531.46-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg20.291
r_dihedral_angle_3_deg13.167
r_dihedral_angle_1_deg6.876
r_angle_refined_deg1.988
r_angle_other_deg0.878
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg20.291
r_dihedral_angle_3_deg13.167
r_dihedral_angle_1_deg6.876
r_angle_refined_deg1.988
r_angle_other_deg0.878
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3460
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms50

Software

Software
Software NamePurpose
Web-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling