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human Myeloid-derived growth factor (MYDGF)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277.15 48% M1K3350 (12% w/v PEG 1000, 12% w/v PEG 3350, and 12% v/v MPD, original solution Molecular Dimensions), 1,25% NPS (3.75 mM sodium nitrate, 3.75 mM sodium phosphate dibasic, and 3.75 mM ammonium sulfate; original solution MolecularDimensions), 0.1M MMT buffer (pH 6.4) (0.02 M DL-malic acid, 0.04 M MES monohydrate, 0.04 M Tris)
Crystal Properties Matthews coefficient Solvent content 2.01 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.677 α = 90 b = 48.677 β = 90 c = 177.846 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 2M-F 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.604 42.155 85.1 0.215 0.215 0.998 11.9 19.1 28207 17.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.604 1.707 25.6 2.299 2.299 0.51 1.3 15
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.604 42.155 28170 1433 83.3 0.219 0.218 0.2123 0.247 0.2077 RANDOM 19.67
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] -0.5971 -0.5971 1.1943
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.34 t_omega_torsion 4.03 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.34 t_omega_torsion 4.03 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion 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 2130 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 7
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling SHELXD phasing