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Crystal Structure of Human Autocrine Motility Factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQR PDB ENTRY 1DQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.77 α = 90 b = 107.4 β = 90 c = 270.7 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 ADSC QUANTUM 4 2000-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B Photon Factory BL-18B
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 1.9 40 98.7 0.108 4.6 7.4 183404
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) 1.9 2 92.1 0.305 2.4 4.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DQR 1.9 36 174100 9195 98.69 0.169 0.16747 0.19791 RANDOM 15.102
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] 0.36 0.68 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.32 r_dihedral_angle_1_deg 4.131 r_scangle_it 2.866 r_scbond_it 1.747 r_angle_refined_deg 1.321 r_mcangle_it 1.089 r_angle_other_deg 0.759 r_mcbond_it 0.59 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.32 r_dihedral_angle_1_deg 4.131 r_scangle_it 2.866 r_scbond_it 1.747 r_angle_refined_deg 1.321 r_mcangle_it 1.089 r_angle_other_deg 0.759 r_mcbond_it 0.59 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.209 r_nbd_other 0.196 r_symmetry_vdw_other 0.174 r_xyhbond_nbd_other 0.151 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17780 Nucleic Acid Atoms Solvent Atoms 1475 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling