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Crystal structure of de novo designed MID1-zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZM PDB ENTRY 1YZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1-2 microliter2 protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 1 microliter crystallization buffer (0.1 M sodium citrate, pH 5.5, 1.25 M ammonium sulfate, 0.08 M K/Na tartrate), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.81 31.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.312 α = 90 b = 29.8 β = 90 c = 105.412 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 CCD MARMOSAIC 300 mm CCD 2011-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9180 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.129 19.292 97.8 0.089 31.4 7.3 30296 30296 -3 -3 9.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.14 88.8 0.49 2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Phaser THROUGHOUT PDB ENTRY 1YZM 1.129 19.292 1.34 30257 30257 1523 97.83 0.1483 0.1468 0.1449 0.1763 0.1759 RANDOM
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] -1.268 0.7055 0.5624
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.84 f_angle_d 1.241 f_chiral_restr 0.072 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 758 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling