X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 294.0
Details 20% PEG3350, 0.2 M NH4 hydrogen Citrate, 2% PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.95 α = 89.04
b = 75.12 β = 90.01
c = 89.49 γ = 75.47
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD MIRROR 2010-08-23
Diffraction Radiation
Monochromator Protocol
Si(111) MOLECULAR REPLACEMENT
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.04006 APS 21-ID-D

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
1.82 30 97.3 0.076 -- -- 3.9 151590 151590 -- -3.0 36.1
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)
1.817 1.85 95.7 0.61 -- 2.2 3.9 7431

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 1.817 29.016 -- 0.0 143966 143966 7600 96.75 -- 0.16369 0.16211 0.19353 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 1.817 1.864 -- 538 9729 0.24 0.291 -- 88.31
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 25.282
Anisotropic B[1][1] 2.02
Anisotropic B[1][2] -0.66
Anisotropic B[1][3] 0.3
Anisotropic B[2][2] -1.48
Anisotropic B[2][3] 1.26
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_bond_refined_d 0.017
r_gen_planes_refined 0.007
r_mcbond_it 0.852
r_scangle_it 4.504
r_mcangle_it 1.567
r_chiral_restr 0.092
r_scbond_it 2.744
r_dihedral_angle_3_deg 13.839
r_dihedral_angle_4_deg 19.184
r_dihedral_angle_2_deg 37.113
r_dihedral_angle_1_deg 5.587
r_gen_planes_other 0.001
r_angle_refined_deg 1.559
r_mcbond_other 0.259
r_angle_other_deg 0.94
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11686
Nucleic Acid Atoms 0
Heterogen Atoms 112
Solvent Atoms 930

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHENIX model building
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing