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crystal structure of the Rho-kinase kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1APM PDB ENTRY 1APM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.8M Sodium Citrate, 0.1M Sodium Citrate Buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.76 67.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.531 α = 90 b = 102.531 β = 90 c = 257.185 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 90 CCD Bruker DIP-6040 a double-crystal monochromator and a horizontal focusing mirror 2003-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.4 30 95.8 0.075 53814 52492
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) 2.4 2.49 81 0.347
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1APM 2.4 30 52481 52481 2663 95.92 0.197 0.197 0.195 0.1911 0.235 0.2311 RANDOM 47.404
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.593 r_dihedral_angle_4_deg 23.701 r_dihedral_angle_3_deg 15.077 r_scangle_it 6.071 r_scbond_it 3.866 r_mcangle_it 2.547 r_dihedral_angle_1_deg 2.384 r_angle_refined_deg 1.681 r_mcbond_it 1.348 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.593 r_dihedral_angle_4_deg 23.701 r_dihedral_angle_3_deg 15.077 r_scangle_it 6.071 r_scbond_it 3.866 r_mcangle_it 2.547 r_dihedral_angle_1_deg 2.384 r_angle_refined_deg 1.681 r_mcbond_it 1.348 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6211 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing