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Crystal Structure of Human Augmenter of Liver Regeneration (ALR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OQC PDB ENTRY 1OQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 18% w/v PEG 8000, 210 mM zinc acetate dihydrate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.719 α = 90 b = 65.145 β = 89.97 c = 63.767 γ = 90
Symmetry Space Group C 1 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 93 IMAGE PLATE RIGAKU RAXIS IV OSMIC BLUE OPTICS 2009-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.85 63.76 99.9 0.044 36.54 3.6 49190
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) 1.85 1.92 100 0.366 3.13 3.6
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 PDB ENTRY 1OQC 1.85 27.76 37427 1975 99.88 0.19129 0.18914 0.187 0.23121 0.2319 RANDOM 29.797
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_3_deg 13.022 r_dihedral_angle_4_deg 12.403 r_dihedral_angle_1_deg 5.196 r_scangle_it 3.874 r_scbond_it 2.338 r_angle_refined_deg 1.889 r_mcangle_it 1.648 r_mcbond_it 0.905 r_symmetry_vdw_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_3_deg 13.022 r_dihedral_angle_4_deg 12.403 r_dihedral_angle_1_deg 5.196 r_scangle_it 3.874 r_scbond_it 2.338 r_angle_refined_deg 1.889 r_mcangle_it 1.648 r_mcbond_it 0.905 r_symmetry_vdw_refined 0.347 r_nbtor_refined 0.305 r_nbd_refined 0.222 r_symmetry_metal_ion_refined 0.187 r_xyhbond_nbd_refined 0.175 r_metal_ion_refined 0.171 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_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 2799 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 217
Software Software Software Name Purpose StructureStudio data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling ARP/wARP model building