X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 291.0
Details PEG 3350, PEG 400, Tris, NaI, glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.09 α = 90
b = 148.78 β = 90
c = 176.71 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-09-05
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.95 45 95.3 -- 0.078 -- -- 94192 94192 1.0 1.0 --
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)
1.95 2.0 95.5 -- 0.35 2.7 -- --

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
FOURIER SYNTHESIS 1.95 20.0 -- 1.0 83301 83301 4465 100.0 -- 0.19075 0.18811 0.23976 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 1.95 2.0 -- 346 5995 0.218 0.276 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.983
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 1.075
r_nbd_other 0.3
r_nbd_refined 0.337
r_gen_planes_other 0.001
r_gen_planes_refined 0.003
r_chiral_restr 0.109
r_dihedral_angle_2_deg 16.507
r_dihedral_angle_1_deg 3.437
r_angle_other_deg 1.275
r_angle_refined_deg 1.25
r_bond_other_d 0.0
r_bond_refined_d 0.008
r_xyhbond_nbd_refined 0.284
r_xyhbond_nbd_other 0.33
r_metal_ion_refined 0.033
r_symmetry_vdw_refined 0.374
r_symmetry_vdw_other 0.297
r_symmetry_hbond_refined 0.323
r_mcbond_it 4.712
r_mcangle_it 6.609
r_scbond_it 10.082
r_scangle_it 13.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7932
Nucleic Acid Atoms 0
Heterogen Atoms 134
Solvent Atoms 853

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement