X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Temperature 293.0
Details 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K
pH 5.5
Temperature 293.0
Details 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 188.68 α = 90
b = 58.86 β = 100.4
c = 89.86 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-13
CCD MARMOSAIC 225 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-13
Diffraction Radiation
Monochromator Protocol
WATER COOLED SI (111) DOUBLE BOUNCE SINGLE WAVELENGTH
CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM -- APS 22-BM
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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
1.86 37.37 98.0 0.066 -- -- 7.0 -- 79505 -- -- --
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)
1.86 1.9 89.5 0.395 -- 3.224 5.1 --

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
SAD 1.86 50.0 -- -- -- 75518 3986 97.7 -- 0.20319 0.201 0.249 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 1.86 1.91 -- 259 4926 0.25 0.343 -- 86.58
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.48
Anisotropic B[1][1] -0.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.22
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.6
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.097
r_nbd_refined 0.221
r_mcbond_it 1.73
r_bond_refined_d 0.017
r_scbond_it 4.837
r_angle_other_deg 16.409
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 16.783
r_mcangle_it 2.948
r_scangle_it 6.843
r_gen_planes_other 0.033
r_xyhbond_nbd_refined 0.162
r_mcbond_other 0.411
r_nbtor_refined 0.312
r_symmetry_vdw_refined 0.198
r_dihedral_angle_1_deg 6.359
r_symmetry_hbond_refined 0.214
r_chiral_restr 0.11
r_nbd_other 0.168
r_nbtor_other 0.288
r_dihedral_angle_2_deg 36.434
r_dihedral_angle_4_deg 17.45
r_angle_refined_deg 1.607
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7122
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 421

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS phasing
RESOLVE phasing version: 2.06
REFMAC refinement version: refmac_5.2.0005
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing version: (HYSS)