☰ Navigation Tabs
Crystal structure of human magnesium-dependent phosphatase 1 of the haloacid dehalogenase superfamily (MGC5987)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1P PDB ENTRY 1U1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M NA3(CIT),20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.34 α = 90 b = 62.34 β = 90 c = 111.86 γ = 90
Symmetry Space Group P 43 21 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 ADSC CCD 2009-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 40 99.9 0.11 15.3 6.2 37274 2
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 1.84 99.9 0.84 2 6.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1U1P 1.75 54.45 21741 1215 99.83 0.16517 0.16341 0.1767 0.19816 0.21 RANDOM 9.697
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] 0.61 0.61 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 17.919 r_dihedral_angle_3_deg 12.908 r_scangle_it 7.651 r_dihedral_angle_1_deg 5.336 r_scbond_it 4.765 r_mcangle_it 2.84 r_mcbond_it 1.577 r_angle_refined_deg 1.139 r_angle_other_deg 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 17.919 r_dihedral_angle_3_deg 12.908 r_scangle_it 7.651 r_dihedral_angle_1_deg 5.336 r_scbond_it 4.765 r_mcangle_it 2.84 r_mcbond_it 1.577 r_angle_refined_deg 1.139 r_angle_other_deg 0.859 r_mcbond_other 0.45 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1381 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing