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human Myeloid-derived growth factor (MYDGF) in complex with neutralizing Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 277.15 0.1 M trisodium citrate (pH 5.5) and 20 % PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.519 α = 71.54 b = 107.43 β = 86.25 c = 109.369 γ = 73.38
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 PILATUS 6M 2019-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999890 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.58 97.82 63.5 0.052 0.052 10.2 2.7 320264 24.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.584 1.584 0.633 0.633 1.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1IQW 1.58 97.82 320264 16013 62.6 0.182 0.181 0.1829 0.206 0.1814 RANDOM 33.23
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] -1.5024 0.9584 1.2789 -1.2375 1.1692 2.7399
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.25 t_omega_torsion 4.09 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_sum_occupancies
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.25 t_omega_torsion 4.09 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24893 Nucleic Acid Atoms Solvent Atoms 2604 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing