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Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like protein (NAALADaseL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.16 M magnesium formate and 16% (w/v) PEG 3350, pH not adjusted
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.512 α = 90 b = 174.844 β = 90 c = 208.034 γ = 90
Symmetry Space Group I 2 2 2
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 225 mm CCD 2009-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 1.75 30 99.7 0.081 9 7.6 177979 -3
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 1.75 1.78 99.4 0.506 7.5 8822
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PVW 1.75 29.14 176202 1757 98.41 0.1676 0.1674 0.1875 0.1952 RANDOM 26.631
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] -0.02 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 14.695 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_1_deg 6.293 r_scangle_it 4.448 r_scbond_it 2.754 r_mcangle_it 1.742 r_angle_refined_deg 1.738 r_mcbond_it 1.015 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 14.695 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_1_deg 6.293 r_scangle_it 4.448 r_scbond_it 2.754 r_mcangle_it 1.742 r_angle_refined_deg 1.738 r_mcbond_it 1.015 r_chiral_restr 0.128 r_bond_refined_d 0.02 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10908 Nucleic Acid Atoms Solvent Atoms 1633 Heterogen Atoms 317
Software Software Software Name Purpose HKL-2000 data reduction SERGUI data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building WARP model building PHASER phasing