X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 294.0
Details 3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.92 α = 90
b = 52.92 β = 90
c = 102.29 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- MIRROR 2009-05-29
Diffraction Radiation
Monochromator Protocol
SI-111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.95 22.33 99.9 0.07 0.07 -- 5.8 23330 23330 -- -3.0 --
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)
1.95 1.98 98.7 0.353 0.353 5.2 5.8 --

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
SAD 1.95 22.33 -- -- 12588 11984 604 99.83 -- 0.18521 0.18316 0.226 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 1.95 2.001 -- 37 839 0.19 0.265 -- 98.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.925
Anisotropic B[1][1] 1.65
Anisotropic B[1][2] 0.82
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.47
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.314
r_dihedral_angle_4_deg 12.846
r_angle_other_deg 0.901
r_chiral_restr 0.098
r_scbond_it 3.529
r_mcangle_it 1.997
r_angle_refined_deg 1.615
r_scangle_it 5.93
r_dihedral_angle_3_deg 12.223
r_dihedral_angle_2_deg 28.8
r_gen_planes_other 0.001
r_bond_refined_d 0.019
r_dihedral_angle_1_deg 5.733
r_bond_other_d 0.001
r_mcbond_it 1.087
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 775
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 105

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
HKL-3000 phasing
MLPHARE phasing
DM model building
SHELXD phasing
ARP/wARP model building
Coot model building
REFMAC refinement version: 5.5.0051
HKL-2000 data reduction
HKL-2000 data scaling
DM phasing