X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 293.0
Details 25% PEG3350, 0.1 M NaCl, 0.1M HEPES-NaOH pH 7.5, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.5 α = 90
b = 59.55 β = 90
c = 67.79 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 315r -- 2008-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9788 ESRF ID29

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
1.45 67.79 95.7 0.043 0.043 -- 3.8 41315 41315 -- -- 18.77
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)
1.45 1.53 93.8 0.377 0.377 2.0 3.5 5806

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 1.45 19.05 -- 0.0 41275 39213 2062 95.16 0.1784 0.1784 0.1769 0.2064 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 1.45 1.488 -- 151 2695 0.24 0.257 -- 91.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.4582
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.1
r_angle_refined_deg 1.546
r_nbtor_refined 0.312
r_dihedral_angle_2_deg 30.618
r_xyhbond_nbd_refined 0.129
r_symmetry_hbond_refined 0.082
r_mcangle_it 1.435
r_bond_refined_d 0.014
r_gen_planes_refined 0.008
r_nbd_refined 0.209
r_scbond_it 2.281
r_dihedral_angle_4_deg 16.59
r_dihedral_angle_3_deg 13.009
r_scangle_it 3.471
r_dihedral_angle_1_deg 6.778
r_symmetry_vdw_refined 0.203
r_mcbond_it 0.954
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1718
Nucleic Acid Atoms 0
Heterogen Atoms 65
Solvent Atoms 223

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.1
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10