X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 25-30% (w/v) PEG3350, 100mM Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.46 α = 90
b = 52.76 β = 95.82
c = 93.64 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR MAR scanner 300 mm plate mirrors --
AREA DETECTOR MAR scanner 300 mm plate mirrors --
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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 46.47 81.34 -- -- -- -- 21606 21606 0.0 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)
1.9 1.95 59.7 0.326 -- 3.2 -- --

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 46.47 -- 0.0 21606 21606 1142 81.34 -- 0.17959 0.17836 0.20252 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 1.9 1.952 -- 69 1159 0.211 0.252 -- 59.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.301
Anisotropic B[1][1] 0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.38
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.064
r_dihedral_angle_4_deg 10.698
r_dihedral_angle_3_deg 11.943
r_dihedral_angle_2_deg 32.624
r_dihedral_angle_1_deg 5.881
r_angle_other_deg 0.7
r_angle_refined_deg 1.097
r_bond_other_d 0.001
r_bond_refined_d 0.006
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.186
Luzzati Sigma A (R-Free Set) 0.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2540
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 162

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SAM-T08 - PHASER - CNS Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
SAM-T08 version: - PHASER - CNS model building
MAR345dtb data collection