X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Temperature 291.0
Details 30% PEG-400, 0.2M lithium sulfate, 0.1M trisodium citrate, pH 5.6, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.62 α = 66.33
b = 74.22 β = 75.53
c = 87.93 γ = 69.62
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-09-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97625 CLSI 08ID-1

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
1.9 50 97.6 0.074 -- -- 3.8 -- 92430 -- -- --
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)
1.9 1.97 96.4 0.848 -- -- 3.7 9089

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
MOLECULAR REPLACEMENT 1.9 50.0 -- 0.0 -- 92179 2066 97.601 -- 0.186 0.1852 0.225 THIN SHELLS (SFTOOLS)
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9 1.949 -- 0 6751 0.287 -- -- 96.264
X Ray Diffraction 1.949 2.003 -- 0 6555 0.267 -- -- 96.624
X Ray Diffraction 2.003 2.061 -- 400 6036 0.25 0.272 -- 96.782
X Ray Diffraction 2.061 2.124 -- 0 6199 0.233 -- -- 96.92
X Ray Diffraction 2.124 2.193 -- 0 6014 0.215 -- -- 96.906
X Ray Diffraction 2.193 2.27 -- 366 5446 0.208 0.256 -- 97.109
X Ray Diffraction 2.27 2.356 -- 0 5679 0.197 -- -- 97.293
X Ray Diffraction 2.356 2.452 -- 290 5173 0.2 0.241 -- 97.658
X Ray Diffraction 2.452 2.56 -- 0 5260 0.199 -- -- 97.715
X Ray Diffraction 2.56 2.685 -- 254 4759 0.194 0.255 -- 98.083
X Ray Diffraction 2.685 2.83 -- 0 4785 0.193 -- -- 98.154
X Ray Diffraction 2.83 3.001 -- 206 4296 0.186 0.215 -- 98.34
X Ray Diffraction 3.001 3.207 -- 0 4283 0.185 -- -- 98.392
X Ray Diffraction 3.207 3.463 -- 151 3841 0.17 0.216 -- 98.544
X Ray Diffraction 3.463 3.792 -- 147 3489 0.159 0.228 -- 98.457
X Ray Diffraction 3.792 4.236 -- 0 3319 0.144 -- -- 98.487
X Ray Diffraction 4.236 4.886 -- 85 2840 0.139 0.182 -- 98.651
X Ray Diffraction 4.886 5.97 -- 76 2411 0.166 0.192 -- 99.4
X Ray Diffraction 5.97 8.383 -- 77 1862 0.194 0.199 -- 99.538
X Ray Diffraction 8.383 50.0 -- 14 1068 0.175 0.271 -- 98.723
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.151
Anisotropic B[1][1] -0.613
Anisotropic B[1][2] -0.549
Anisotropic B[1][3] -0.243
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] 0.72
Anisotropic B[3][3] 0.279
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.004
r_chiral_restr 0.061
r_dihedral_angle_4_deg 15.459
r_dihedral_angle_3_deg 11.886
r_dihedral_angle_2_deg 34.518
r_dihedral_angle_1_deg 5.408
r_angle_other_deg 0.808
r_angle_refined_deg 1.407
r_bond_other_d 0.003
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7479
Nucleic Acid Atoms 0
Heterogen Atoms 188
Solvent Atoms 354

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
Phaser molecular replacement
HKL data reduction