2I5T

Crystal Structure of hypothetical protein LOC79017 from Homo sapiens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BISTRIS PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (28% PEG 2K, 0.20 M POTASSIUM GLUTAMATE, 0.1 M MES/ACETATE PH 5.5) CRYOPROTECTED WITH 10% ETHYLENE GLYCOL IN WELL SOLUTION, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.242.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.052α = 90
b = 100.138β = 90
c = 102.498γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY2006-06-18MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.0145.62197.50.12312.18510.824297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0883.20.3574.0968.1

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 DIFFRACTIONSADTHROUGHOUT2.0145.6224213123397.50.1860.1830.234RANDOM23.54
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]
-0.4361.092-0.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.927
r_dihedral_angle_3_deg14.676
r_dihedral_angle_4_deg8.502
r_scangle_it7.909
r_dihedral_angle_1_deg6.117
r_scbond_it5.535
r_mcangle_it3.012
r_mcbond_it2.711
r_angle_refined_deg1.506
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.927
r_dihedral_angle_3_deg14.676
r_dihedral_angle_4_deg8.502
r_scangle_it7.909
r_dihedral_angle_1_deg6.117
r_scbond_it5.535
r_mcangle_it3.012
r_mcbond_it2.711
r_angle_refined_deg1.506
r_nbtor_refined0.309
r_symmetry_hbond_refined0.265
r_nbd_refined0.209
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.134
r_chiral_restr0.114
r_bond_refined_d0.02
r_gen_planes_refined0.007
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2681
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction