X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details Ammonium phosphate, sodium hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.92 α = 90
b = 118.63 β = 90
c = 136.3 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 MARRESEARCH Mirrors 2002-03-10
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14

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
1.7 20 98.3 -- 0.048 -- 4.0 85290 85290 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)
1.7 1.79 97.2 0.268 0.268 2.8 3.7 --

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
SAD 1.8 20.0 -- 2.0 85290 80019 2468 89.52 0.1598 0.15985 0.15889 0.19084 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 1.8 1.846 -- 131 4561 0.182 0.228 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.157
Anisotropic B[1][1] 2.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.9
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.25
r_scbond_it 2.836
r_mcangle_it 1.702
r_mcbond_it 1.028
r_symmetry_hbond_refined 0.532
r_symmetry_vdw_other 0.171
r_symmetry_vdw_refined 0.138
r_bond_refined_d 0.021
r_bond_other_d 0.002
r_angle_refined_deg 1.749
r_angle_other_deg 0.916
r_dihedral_angle_1_deg 6.26
r_chiral_restr 0.114
r_gen_planes_refined 0.01
r_gen_planes_other 0.008
r_nbd_refined 0.224
r_nbd_other 0.249
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.172
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6432
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 540

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement