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Crystal structure of human NM23-H1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 6.5% PEG 8000, 0.1M Na/K Phosphate pH 6.2, 0.2 NaCl,0.2M NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.31 62.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.51 α = 90 b = 154.51 β = 90 c = 111.821 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 315r 2008-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 63.51 100 46177 1 1
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 1UCN 2.1 50 43752 2337 99.57 0.22448 0.22356 0.2226 0.24193 0.2417 RANDOM 28.982
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] 0.65 0.32 0.65 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 21.562 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 4.506 r_angle_refined_deg 0.897 r_scangle_it 0.737 r_mcangle_it 0.424 r_scbond_it 0.412 r_mcbond_it 0.227 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 21.562 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 4.506 r_angle_refined_deg 0.897 r_scangle_it 0.737 r_mcangle_it 0.424 r_scbond_it 0.412 r_mcbond_it 0.227 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3634 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 10
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling