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Human nucleoside diphosphate kinase A complexed with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UCN PDB ENTRY 1UCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 2.4 M AMMONIUM SULPHATE,10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.26 α = 90 b = 114.26 β = 90 c = 89.789 γ = 90
Symmetry Space Group P 41 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 MARRESEARCH 2005-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.973 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 17.65 97.2 0.08 10.2 3.2 30827 30827 39.084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 99 0.52 3.1 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1UCN 2.15 17.65 30827 30827 1639 98.75 0.24911 0.24911 0.24672 0.29374 0.3076 RANDOM 42.196
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] -0.69 -0.69 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_4_deg 22.99 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 6.298 r_scangle_it 2.084 r_scbond_it 1.514 r_angle_refined_deg 1.299 r_mcbond_it 1.132 r_mcangle_it 1.033 r_angle_other_deg 0.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_4_deg 22.99 r_dihedral_angle_3_deg 14.412 r_dihedral_angle_1_deg 6.298 r_scangle_it 2.084 r_scbond_it 1.514 r_angle_refined_deg 1.299 r_mcbond_it 1.132 r_mcangle_it 1.033 r_angle_other_deg 0.787 r_symmetry_vdw_refined 0.388 r_symmetry_vdw_other 0.202 r_nbd_refined 0.197 r_nbd_other 0.194 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.172 r_mcbond_other 0.1 r_symmetry_hbond_refined 0.088 r_nbtor_other 0.084 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.021 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3594 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 81
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction CCP4 data scaling