X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 291.0
Details 6% PEG3350, 100mM CsCl, 100 mM sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.65 α = 90
b = 98.65 β = 90
c = 89.75 γ = 120
Symmetry
Space Group P 3 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2007-09-25
Diffraction Radiation
Monochromator Protocol
YALE MIrrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.54178 -- --

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
2.6 20 99.2 0.095 -- -- 8.0 15619 15494 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)
2.6 2.69 96.9 0.927 -- 1.5 5.8 --

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 2.6 20.0 -- -- 15494 14685 773 98.91 -- 0.20392 0.19998 0.28239 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 2.596 2.663 -- 57 1042 0.381 0.426 -- 95.57
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.11
Anisotropic B[1][1] 0.62
Anisotropic B[1][2] 0.31
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.93
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 9.848
r_scbond_it 6.862
r_mcangle_it 3.986
r_mcbond_it 2.545
r_nbd_refined 0.317
r_gen_planes_refined 0.024
r_chiral_restr 0.163
r_dihedral_angle_4_deg 22.803
r_dihedral_angle_3_deg 23.069
r_dihedral_angle_2_deg 42.47
r_dihedral_angle_1_deg 8.554
r_angle_refined_deg 2.407
r_bond_refined_d 0.012
r_nbtor_refined 0.35
r_xyhbond_nbd_refined 0.228
r_symmetry_vdw_refined 0.351
r_symmetry_hbond_refined 0.316
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.44
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3227
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 127

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
CNS version: 1.2 refinement