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Fluorescent Protein mKeima at pH 5.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P4M PDB ENTRY 2P4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 293 21% PEG 6000, 0.4M NACL, 0.15M SODIUM PHOSPHATE PH5.6, VAPOR DIFFUSION, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 227.457 α = 90 b = 55.565 β = 108.47 c = 90.562 γ = 90
Symmetry Space Group C 1 2 1
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 2008-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.9 45.1 99.6 0.14 11.8 3.6 80367 21.72
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 1.9 2.02 98.5 0.65 4 3.6
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 2P4M 1.9 45.13 80367 4256 99.57 0.18544 0.18261 0.1832 0.23886 0.2398 RANDOM 17.398
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] -1.03 -0.97 1.05 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.061 r_dihedral_angle_4_deg 18.845 r_dihedral_angle_3_deg 14.758 r_dihedral_angle_1_deg 6.84 r_scangle_it 3.58 r_scbond_it 2.428 r_angle_refined_deg 1.827 r_mcangle_it 1.381 r_mcbond_it 1.208 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.061 r_dihedral_angle_4_deg 18.845 r_dihedral_angle_3_deg 14.758 r_dihedral_angle_1_deg 6.84 r_scangle_it 3.58 r_scbond_it 2.428 r_angle_refined_deg 1.827 r_mcangle_it 1.381 r_mcbond_it 1.208 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.241 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 6940 Nucleic Acid Atoms Solvent Atoms 1303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing