X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70 α = 90
b = 68.74 β = 90
c = 74 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Dynamically bendable mirror 2009-05-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.000000 SLS X10SA

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
2.1 45 99.1 0.091 -- -- 4.02 21461 21265 -- -3.0 26.761
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)
2.1 2.2 99.8 0.445 -- 5.5 4.06 2758

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 2.1 40.89 -- 0.0 21461 21265 851 100.0 -- 0.213 0.21 0.273 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 2.1 2.154 -- 62 1490 0.248 0.363 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.738
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.161
r_xyhbond_nbd_refined 0.18
r_symmetry_hbond_refined 0.112
r_angle_refined_deg 1.638
r_scbond_it 2.455
r_dihedral_angle_2_deg 36.238
r_scangle_it 3.867
r_gen_planes_refined 0.005
r_chiral_restr 0.109
r_mcangle_it 1.727
r_nbtor_refined 0.314
r_dihedral_angle_1_deg 6.188
r_mcbond_it 1.008
r_dihedral_angle_3_deg 18.001
r_nbd_refined 0.222
r_dihedral_angle_4_deg 17.275
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2727
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 126

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 1.3.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
XDS data scaling
XDS data reduction