X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 293.0
Details 30% PEGMME 2000, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.43 α = 90
b = 89.97 β = 102.25
c = 62.84 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-02-10
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A

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
1.88 61.41 98.3 0.085 -- -- 6.9 -- 45454 -- -- 29.4
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)
1.9 1.97 89.7 0.267 -- 5.4 5.6 4112

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 1.88 50.0 -- -- -- 43068 2306 96.66 -- 0.19762 0.19548 0.23771 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 1.884 1.933 -- 120 2247 0.246 0.306 -- 67.69
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.537
Anisotropic B[1][1] 3.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.42
Anisotropic B[2][2] -0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.809
r_mcangle_it 1.591
r_mcbond_it 0.907
r_gen_planes_refined 0.007
r_bond_refined_d 0.017
r_chiral_restr 0.114
r_scbond_it 2.519
r_dihedral_angle_2_deg 41.232
r_dihedral_angle_4_deg 17.295
r_angle_refined_deg 1.538
r_dihedral_angle_3_deg 13.298
r_scangle_it 4.029
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5012
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 373

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
MOLREP phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling