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Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) from uncultured marine organism at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 9 277 30.0% PEG-6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.433 α = 90 b = 92.842 β = 90 c = 144.927 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 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2006-11-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97944, 0.97972 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 29.086 99.8 0.072 0.072 6.1 3.6 42961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 0.611 0.611 1.2 3.6 3134
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.85 29.086 42910 2164 99.68 0.198 0.197 0.1988 0.231 0.2335 RANDOM 11.009
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] 4.05 -2.58 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.353 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_4_deg 13.632 r_scangle_it 6.948 r_dihedral_angle_1_deg 6.753 r_scbond_it 5.681 r_mcangle_it 3.122 r_mcbond_it 2.465 r_angle_refined_deg 1.681 r_angle_other_deg 1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.353 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_4_deg 13.632 r_scangle_it 6.948 r_dihedral_angle_1_deg 6.753 r_scbond_it 5.681 r_mcangle_it 3.122 r_mcbond_it 2.465 r_angle_refined_deg 1.681 r_angle_other_deg 1.061 r_mcbond_other 0.716 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.212 r_nbd_other 0.197 r_nbtor_refined 0.19 r_symmetry_vdw_other 0.184 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.136 r_nbtor_other 0.093 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.017 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 3468 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 120
Software Software Software Name Purpose MolProbity model building SOLVE phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling