X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 283.0
Details 0.1M TEA pH 7.5, 20% PEG 400, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.65 α = 90
b = 116.65 β = 90
c = 44.09 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-11-23
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.514 -- --

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
2.25 25 94.3 0.066 -- -- 3.9 -- 13458 2.0 2.0 --
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)
2.25 2.33 65.4 0.185 -- -- 3.1 926

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 2.25 23.81 -- 0.0 13478 12793 685 100.0 0.197 0.197 0.194 0.261 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 2.251 2.309 680 33 647 0.173 0.276 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.254
Anisotropic B[1][1] -1.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.85
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.183
r_symmetry_vdw_refined 0.211
r_scbond_it 3.029
r_dihedral_angle_3_deg 17.411
r_gen_planes_refined 0.009
r_bond_refined_d 0.021
r_dihedral_angle_4_deg 17.049
r_symmetry_hbond_refined 0.199
r_mcangle_it 2.033
r_nbd_refined 0.223
r_dihedral_angle_1_deg 7.255
r_dihedral_angle_2_deg 34.126
r_angle_refined_deg 1.788
r_chiral_restr 0.125
r_xyhbond_nbd_refined 0.197
r_nbtor_refined 0.322
r_mcbond_it 1.187
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1949
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 100

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
MOLREP phasing