X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 17% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.8 α = 90
b = 54.8 β = 105
c = 75.8 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SATURN -- 2007-04-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5417 -- --

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
1.6 20 96.0 0.033 -- -- 6.4 -- 59358 -- -3.0 26.066
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)
1.6 1.7 81.7 0.441 -- 3.1 -- --

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 1.6 19.63 -- 0.0 -- 59357 3001 96.18 -- 0.203 0.202 0.232 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 1.6 1.642 -- 175 3206 0.282 0.346 -- 74.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.446
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.891
r_nbtor_refined 0.294
r_bond_refined_d 0.012
r_dihedral_angle_2_deg 31.848
r_gen_planes_refined 0.006
r_symmetry_vdw_refined 0.121
r_symmetry_hbond_refined 0.124
r_chiral_restr 0.1
r_angle_refined_deg 1.308
r_mcangle_it 1.386
r_mcbond_it 0.916
r_scangle_it 3.286
r_xyhbond_nbd_refined 0.127
r_dihedral_angle_1_deg 5.755
r_dihedral_angle_3_deg 11.898
r_scbond_it 2.224
r_nbd_refined 0.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3157
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 400

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.004
XDS data reduction
MOLREP phasing