1SJ5

Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 2.8 A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.9
Details pH 6.90

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44 α = 90
b = 52.14 β = 97.64
c = 73.33 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

Data Collection

Overall
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
2.8 72.55 98.2 -- 0.079 -- -- -- 8172 -- 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.8 2.9 98.9 -- 0.652 3.1 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 2.8 72.55 -- 0.0 -- 7762 349 98.2 -- 0.21858 0.21571 0.27555 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.388
Anisotropic B[1][1] -3.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.26
Anisotropic B[2][2] 1.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.64
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.232
r_chiral_restr 0.081
r_symmetry_hbond_refined 0.323
r_nbd_other 0.231
r_scangle_it 4.847
r_dihedral_angle_1_deg 7.853
r_nbtor_other 0.088
r_bond_refined_d 0.017
r_bond_other_d 0.003
r_angle_other_deg 0.878
r_scbond_it 3.309
r_symmetry_vdw_other 0.28
r_symmetry_vdw_refined 0.211
r_mcangle_it 1.061
r_xyhbond_nbd_refined 0.159
r_mcbond_it 0.441
r_gen_planes_other 0.007
r_gen_planes_refined 0.006
r_angle_refined_deg 1.635
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2173
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CCP4 model building version: PACKAGE
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
CCP4 phasing