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Crystal Structure of the L27 domain of Discs Large 1 (target ID NYSGRC-010766) from Drosophila melanogaster (space group P212121)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 0.2 M Sodium Format, 20 % PEG 3350, 3 % 1,8-Diaminooctane, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.958 α = 90 b = 57.698 β = 90 c = 64.632 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315 2013-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.42 30 95.9 0.095 15.9 15 35614 33288
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 1.42 1.44 94.5 0.934 8.1 1623
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 (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 4RP3 1.42 28.21 32994 31575 1671 95.7 0.1505 0.1478 0.1457 0.1984 0.1955 RANDOM 27.398
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] -0.66 0.88 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_sphericity_free 30.319 r_sphericity_bonded 18.202 r_dihedral_angle_4_deg 16.924 r_dihedral_angle_3_deg 13.327 r_rigid_bond_restr 6.726 r_dihedral_angle_1_deg 5.014 r_mcangle_it 4.04 r_mcbond_it 3.659 r_mcbond_other 3.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_sphericity_free 30.319 r_sphericity_bonded 18.202 r_dihedral_angle_4_deg 16.924 r_dihedral_angle_3_deg 13.327 r_rigid_bond_restr 6.726 r_dihedral_angle_1_deg 5.014 r_mcangle_it 4.04 r_mcbond_it 3.659 r_mcbond_other 3.656 r_angle_refined_deg 2.058 r_angle_other_deg 0.949 r_chiral_restr 0.125 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1501 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-3000 data reduction PHASER phasing