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Crystal structure of the RRM domain of mouse Deleted in azoospermia- like in complex with Sycp3 RNA, UUGUUU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XS2 PDB ENTRY 2XS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 MM MAGNESIUM FORMATE, 25% (W/V) PEG 3350 10 MM ZINC ACETATE
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.888 α = 90 b = 37.749 β = 90 c = 70.771 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 ADSC CCD KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING 2010-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.45 29.82 99.1 0.08 16.1 6.9 16096 6 15.2
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 1.45 1.53 97.7 0.92 2.1 6.1
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 2XS2 1.45 29.83 15097 999 99.15 0.16471 0.16207 0.1605 0.20469 0.2025 RANDOM 18.568
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] 0.82 -0.72 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.606 r_dihedral_angle_4_deg 14.401 r_dihedral_angle_3_deg 10.158 r_dihedral_angle_1_deg 6.374 r_scangle_it 4.893 r_scbond_it 3.541 r_mcangle_it 2.379 r_rigid_bond_restr 1.723 r_angle_refined_deg 1.615 r_mcbond_it 1.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.606 r_dihedral_angle_4_deg 14.401 r_dihedral_angle_3_deg 10.158 r_dihedral_angle_1_deg 6.374 r_scangle_it 4.893 r_scbond_it 3.541 r_mcangle_it 2.379 r_rigid_bond_restr 1.723 r_angle_refined_deg 1.615 r_mcbond_it 1.395 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.118 r_symmetry_metal_ion_refined 0.109 r_chiral_restr 0.1 r_metal_ion_refined 0.055 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 673 Nucleic Acid Atoms 84 Solvent Atoms 103 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing