X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 1.7 M ammonium sulfate, 0.1M acetate buffer pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.57 α = 90
b = 96.57 β = 90
c = 143.8 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 MAR CCD 165 mm -- 2010-05-31
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 X13 0.8123 EMBL/DESY, HAMBURG X13

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
2.31 50 94.6 0.087 -- -- 6.5 -- 31502 -- -3.0 48.8
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)
2.31 2.39 68.7 0.521 -- 1.93 2.8 2269

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 2.32 50.0 -- 0.0 31502 31495 1033 98.9 0.19914 0.19913 0.19712 0.25852 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 2.32 2.379 -- 76 2189 0.533 0.571 -- 94.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.844
Anisotropic B[1][1] 1.76
Anisotropic B[1][2] 0.88
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.64
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.12
r_scbond_it 2.661
r_mcangle_it 1.475
r_mcbond_it 0.803
r_gen_planes_refined 0.009
r_chiral_restr 0.139
r_dihedral_angle_4_deg 26.304
r_dihedral_angle_3_deg 20.736
r_dihedral_angle_2_deg 37.441
r_dihedral_angle_1_deg 6.72
r_angle_refined_deg 2.093
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4609
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 270

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