X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details 11-14% PEG 4K, 0.1 M NA ACETATE, 0.2 M AMMONIUM ACETATE. CRYO - 25% ETHYLENE GLYCOL, 10-13 MG/ML PROTEIN, pH 4.60

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.04 α = 90
b = 168.04 β = 90
c = 95.74 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD TOROIDAL MIRROR 2003-06-15
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL, SI(111) OR SI (311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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 40 99.0 0.102 -- -- 5.3 -- 110958 -- -- --
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 2.02 99.2 0.371 -- 2.95 4.4 --

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 1.95 141.42 -- -- -- 102716 5361 96.0 -- 0.194 0.193 0.229 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 2.0 -- 369 7095 0.278 0.332 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.95
Anisotropic B[1][1] -0.79
Anisotropic B[1][2] -0.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.18
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.134
r_chiral_restr 0.107
r_nbd_refined 0.201
r_gen_planes_refined 0.006
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.122
r_mcangle_it 1.361
r_scbond_it 2.178
r_dihedral_angle_1_deg 5.911
r_angle_refined_deg 1.385
r_symmetry_vdw_refined 0.157
r_mcbond_it 0.73
r_scangle_it 3.343
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7878
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 881

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing