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Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.68 53.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.281 α = 90 b = 71.979 β = 90 c = 115.346 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1998-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.45 25 99 0.046 16 4.2 17048 15482 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 99.2 0.161
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FLT 2.45 20 -3 16661 15482 1153 100 0.19843 0.19843 0.19367 0.1898 0.26022 0.2516 RANDOM 12.659
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] -0.78 -0.95 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_3_deg 18.714 r_dihedral_angle_4_deg 17.083 r_dihedral_angle_1_deg 6.686 r_scangle_it 5.405 r_mcangle_it 4.649 r_scbond_it 3.749 r_mcbond_it 3.008 r_angle_refined_deg 1.556 r_nbd_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_3_deg 18.714 r_dihedral_angle_4_deg 17.083 r_dihedral_angle_1_deg 6.686 r_scangle_it 5.405 r_mcangle_it 4.649 r_scbond_it 3.749 r_mcbond_it 3.008 r_angle_refined_deg 1.556 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2985 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing