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Crystal structure of NRP2 in complex with aNRP2-10 Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 21% PEG1000, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 0.05M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.424 α = 90 b = 225.164 β = 91.3 c = 142.996 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 50 90.9 0.274 0.298 0.116 0.957 4.33 6.3 66035 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 89.3 1.247 1.352 0.517 0.434 1 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.205 49.65 62689 3309 90.56 0.25 0.2477 0.2486 0.2941 0.2947 87.439
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] -1.018 -0.975 1.911 -0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.159 r_lrange_it 18.386 r_lrange_other 18.386 r_dihedral_angle_6_deg 17.832 r_mcangle_other 10.371 r_mcangle_it 10.37 r_scangle_it 9.588 r_scangle_other 9.588 r_dihedral_angle_1_deg 6.879 r_mcbond_it 6.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.159 r_lrange_it 18.386 r_lrange_other 18.386 r_dihedral_angle_6_deg 17.832 r_mcangle_other 10.371 r_mcangle_it 10.37 r_scangle_it 9.588 r_scangle_other 9.588 r_dihedral_angle_1_deg 6.879 r_mcbond_it 6.311 r_mcbond_other 6.31 r_dihedral_angle_2_deg 5.769 r_scbond_it 5.715 r_scbond_other 5.715 r_angle_refined_deg 1.313 r_angle_other_deg 0.477 r_symmetry_nbd_refined 0.334 r_nbd_other 0.316 r_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.222 r_nbd_refined 0.207 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.165 r_ncsr_local_group_10 0.131 r_ncsr_local_group_16 0.126 r_ncsr_local_group_2 0.123 r_ncsr_local_group_1 0.112 r_ncsr_local_group_3 0.11 r_ncsr_local_group_11 0.103 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.062 r_ext_dist_refined_b 0.049 r_ncsr_local_group_4 0.029 r_ncsr_local_group_6 0.028 r_ncsr_local_group_12 0.027 r_ncsr_local_group_17 0.026 r_ncsr_local_group_5 0.02 r_ncsr_local_group_14 0.017 r_ncsr_local_group_7 0.016 r_ncsr_local_group_15 0.016 r_ncsr_local_group_13 0.013 r_ncsr_local_group_18 0.011 r_ncsr_local_group_9 0.01 r_ncsr_local_group_8 0.009 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26621 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing