2OD5

CRYSTAL STRUCTURE OF A PUTATIVE NUCLEIC ACID BINDING PROTEIN (JCVI_PEP_1096688149193) FROM UNCULTURED MARINE ORGANISM AT 1.79 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP72771.0M LiCl, 20.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0259.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.406α = 90
b = 64.406β = 90
c = 133.246γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2006-11-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97971SSRLBL11-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.628.9891000.1370.1373.913.616175
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)RedundancyNumber Unique Reflections (All)
11.791.841000.0171.6740.4141154

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.7928.9891612780999.930.190.1890.213RANDOM31.725
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.394
r_dihedral_angle_3_deg12.595
r_scangle_it6.743
r_dihedral_angle_1_deg5.664
r_scbond_it5.253
r_dihedral_angle_4_deg4.303
r_mcangle_it3.437
r_mcbond_it2.378
r_angle_refined_deg1.418
r_angle_other_deg0.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.394
r_dihedral_angle_3_deg12.595
r_scangle_it6.743
r_dihedral_angle_1_deg5.664
r_scbond_it5.253
r_dihedral_angle_4_deg4.303
r_mcangle_it3.437
r_mcbond_it2.378
r_angle_refined_deg1.418
r_angle_other_deg0.954
r_mcbond_other0.529
r_symmetry_vdw_other0.309
r_symmetry_vdw_refined0.253
r_symmetry_hbond_refined0.235
r_nbd_refined0.227
r_nbd_other0.198
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.148
r_chiral_restr0.093
r_nbtor_other0.087
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms720
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms45

Software

Software
Software NamePurpose
MolProbitymodel building
SOLVEphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling