X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 297.0
Details 100 mM Tris 15% polyethylene glycol 8000, 60 mM NaF, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.41 α = 90
b = 59.19 β = 98.36
c = 60.66 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 140
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2006-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --

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
1.9 50 99.1 -- 0.059 -- 6.8 2657 26330 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)
1.9 1.95 99.7 -- -- -- -- --

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
MOLECULAR REPLACEMENT 1.9 50.0 -- 1.0 26569 26330 1408 99.08 -- 0.18046 0.17841 0.21901 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 1.9 1.949 -- 106 1922 0.184 0.236 -- 97.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.51
Anisotropic B[1][1] 0.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.58
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.46
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.724
r_symmetry_vdw_refined 0.213
r_dihedral_angle_1_deg 9.92
r_mcangle_it 1.464
r_scbond_it 2.541
r_dihedral_angle_4_deg 17.852
r_gen_planes_refined 0.006
r_nbtor_refined 0.303
r_dihedral_angle_2_deg 38.973
r_nbd_refined 0.223
r_scangle_it 4.051
r_symmetry_hbond_refined 0.273
r_mcbond_it 0.912
r_xyhbond_nbd_refined 0.153
r_bond_refined_d 0.016
r_dihedral_angle_3_deg 15.395
r_chiral_restr 0.247
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2784
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 219

Software

Software
Software Name Purpose
HKL-2000 data collection
CCP4 model building
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling
CCP4 phasing