2QQJ

Crystal Structure of the b1b2 Domains from Human Neuropilin-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QQIPDB entry 2QQI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52970.1 M Bis-Tris, 20% PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.456α = 90
b = 70.501β = 90
c = 121.929γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.00ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.955099.80.08916.85.32369132.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0299.90.533.15.22349

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 2QQI1.952022404121699.860.1760.1720.235RANDOM22.462
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]
2.74-1.22-1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.482
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg12.992
r_dihedral_angle_1_deg7.326
r_scangle_it4.494
r_mcangle_it4.033
r_mcbond_it3.43
r_scbond_it3.358
r_angle_refined_deg1.454
r_angle_other_deg0.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.482
r_dihedral_angle_4_deg16.608
r_dihedral_angle_3_deg12.992
r_dihedral_angle_1_deg7.326
r_scangle_it4.494
r_mcangle_it4.033
r_mcbond_it3.43
r_scbond_it3.358
r_angle_refined_deg1.454
r_angle_other_deg0.935
r_mcbond_other0.72
r_symmetry_vdw_other0.234
r_nbd_other0.201
r_symmetry_hbond_refined0.191
r_nbd_refined0.181
r_nbtor_refined0.174
r_symmetry_vdw_refined0.148
r_xyhbond_nbd_refined0.121
r_chiral_restr0.091
r_nbtor_other0.084
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2503
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction