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The apo structure of Orf1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.43 64.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.694 α = 90.121 b = 108.507 β = 89.951 c = 134.911 γ = 83.754
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300-HS 2021-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.47 30 97.5 0.058 0.066 0.031 23.4 4.4 201246
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.56 93 0.41 0.465 0.217 3.2 4.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7XQA 2.482 29.669 195367 9539 94.509 0.221 0.2196 0.247 0.2426 41.725
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] -0.198 -0.403 0.028 0.235 -0.046 -0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_3_deg 16.699 r_dihedral_angle_4_deg 16.021 r_lrange_it 7.143 r_lrange_other 7.141 r_dihedral_angle_1_deg 6.716 r_scangle_it 5.175 r_scangle_other 5.175 r_mcangle_it 4.685 r_mcangle_other 4.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_3_deg 16.699 r_dihedral_angle_4_deg 16.021 r_lrange_it 7.143 r_lrange_other 7.141 r_dihedral_angle_1_deg 6.716 r_scangle_it 5.175 r_scangle_other 5.175 r_mcangle_it 4.685 r_mcangle_other 4.685 r_scbond_it 3.233 r_scbond_other 3.232 r_mcbond_it 3.042 r_mcbond_other 3.042 r_angle_refined_deg 1.404 r_angle_other_deg 1.225 r_nbd_other 0.24 r_symmetry_nbd_refined 0.198 r_nbd_refined 0.189 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.062 r_ncsr_local_group_24 0.059 r_ncsr_local_group_15 0.058 r_ncsr_local_group_25 0.054 r_ncsr_local_group_2 0.052 r_ncsr_local_group_6 0.052 r_ncsr_local_group_19 0.052 r_ncsr_local_group_10 0.051 r_ncsr_local_group_12 0.051 r_ncsr_local_group_28 0.051 r_ncsr_local_group_13 0.05 r_ncsr_local_group_18 0.049 r_ncsr_local_group_26 0.049 r_ncsr_local_group_7 0.048 r_ncsr_local_group_8 0.048 r_ncsr_local_group_9 0.048 r_ncsr_local_group_21 0.048 r_ncsr_local_group_16 0.047 r_ncsr_local_group_27 0.047 r_ncsr_local_group_3 0.046 r_ncsr_local_group_14 0.046 r_ncsr_local_group_20 0.045 r_ncsr_local_group_23 0.045 r_ncsr_local_group_1 0.044 r_ncsr_local_group_5 0.039 r_ncsr_local_group_4 0.028 r_ncsr_local_group_11 0.026 r_ncsr_local_group_22 0.021 r_ncsr_local_group_17 0.019 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29166 Nucleic Acid Atoms Solvent Atoms 743 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing