X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.7
Temperature 298.0
Details 0.1M Bis-Tris pH5.7, 0.3M NaCl, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.35 α = 90
b = 85.96 β = 102.02
c = 77.33 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2013-01-03
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.92 DIAMOND I04

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
2.12 37.82 97.9 0.061 0.07 -- 4.1 54454 54303 2.6 2.6 32.0
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)
2.16 37.81 99.2 0.572 0.65 2.6 4.3 7984

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 2.12 37.4 2.0 -- 54303 51526 2755 97.7 0.266 0.26548 0.26449 0.28348 RANDOM
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 2.12 2.175 34042 207 3825 0.333 0.349 0.012 99.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.666
Anisotropic B[1][1] -2.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.56
Anisotropic B[2][2] -2.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.08
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.41
r_sphericity_free 31.054
r_bond_refined_d 0.006
r_bond_other_d 0.002
r_angle_refined_deg 1.303
r_angle_other_deg 0.914
r_dihedral_angle_1_deg 7.318
r_dihedral_angle_2_deg 36.468
r_dihedral_angle_3_deg 19.41
r_dihedral_angle_4_deg 16.765
r_chiral_restr 0.08
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_rigid_bond_restr 2.654
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.02
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 2.16
Luzzati ESD (R-Free Set) 0.03
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7035
Nucleic Acid Atoms 840
Heterogen Atoms 0
Solvent Atoms 163

Software

Computing
Computing Package Purpose
Imosflm Data Collection
Scala Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
Phaser model building
Imosflm data collection