X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 289.0
Details 18-20% PEG 20000, 0.1M pH 8.5 Tris-Hcl, microbatch, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.41 α = 90
b = 95.6 β = 90
c = 97.88 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 4 Bent cylindrical mirror 2005-12-15
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.980 ESRF ID23-2

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
2.95 68.36 99.1 0.094 0.094 -- 5.3 -- 15109 2.0 2.0 73.7
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)
2.95 3.03 99.3 0.369 0.369 5.2 5.5 1087

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 2.95 68.36 0.0 0.0 15109 14309 755 98.83 0.22706 0.22706 0.22428 0.28074 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 2.95 3.026 1087 71 1010 0.265 0.359 -- 99.17
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.348
Anisotropic B[1][1] 1.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.82
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 20.405
r_xyhbond_nbd_refined 0.169
r_symmetry_hbond_refined 0.181
r_mcbond_it 0.696
r_chiral_restr 0.101
r_scangle_it 3.052
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 18.861
r_gen_planes_refined 0.005
r_nbd_refined 0.246
r_nbtor_refined 0.323
r_dihedral_angle_2_deg 36.008
r_mcangle_it 1.234
r_symmetry_vdw_refined 0.243
r_angle_refined_deg 1.713
r_dihedral_angle_1_deg 6.527
r_scbond_it 1.799
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5179
Nucleic Acid Atoms 84
Heterogen Atoms 48
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ADSC data collection version: QUANTUM
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MOLREP phasing