3DJV

Bovine Seminal Ribonuclease- cytidine 3' phosphate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R5DPDB ENTRY 1R5D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528930% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.355α = 90
b = 58.997β = 90
c = 81.994γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8088EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.627.697.90.03626.24.93112031086-316.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6385.10.2735.43.77804

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1R5D1.627.63112029510157597.640.178090.176670.20363RANDOM13.69
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]
0.03-0.20.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.209
r_dihedral_angle_3_deg11.618
r_dihedral_angle_4_deg8.804
r_dihedral_angle_1_deg5.542
r_scangle_it2.394
r_scbond_it1.485
r_angle_refined_deg1.342
r_mcangle_it0.895
r_mcbond_it0.512
r_nbtor_refined0.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.209
r_dihedral_angle_3_deg11.618
r_dihedral_angle_4_deg8.804
r_dihedral_angle_1_deg5.542
r_scangle_it2.394
r_scbond_it1.485
r_angle_refined_deg1.342
r_mcangle_it0.895
r_mcbond_it0.512
r_nbtor_refined0.289
r_nbd_refined0.187
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.11
r_chiral_restr0.09
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1882
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing