X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 80% Tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.25 α = 90
b = 89.25 β = 90
c = 134.8 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2011-08-21
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9320 EMBL/DESY, HAMBURG X12

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
2.04 50 99.9 0.11 -- -- 7.0 -- 38668 0.0 -3.0 --
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)
2.04 2.11 99.2 0.639 -- 2.1 5.4 --

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 2.04 50.0 -- -- 38668 37399 1211 99.84 -- 0.19756 0.19612 0.24294 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 2.04 2.093 -- 87 2732 0.33 0.366 -- 98.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.582
Anisotropic B[1][1] 1.99
Anisotropic B[1][2] 0.99
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.98
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 22.427
r_dihedral_angle_2_deg 34.897
r_chiral_restr 0.11
r_scangle_it 3.946
r_mcbond_it 0.825
r_angle_refined_deg 1.966
r_mcangle_it 1.445
r_bond_refined_d 0.021
r_dihedral_angle_1_deg 6.225
r_scbond_it 2.557
r_gen_planes_refined 0.009
r_dihedral_angle_3_deg 16.735
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4609
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 345

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
HKL-2000 data collection