X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 279.0
Details 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.2 α = 90
b = 48.2 β = 90
c = 63.21 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER PROTEUM multi-layer optics 2005-01-22
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE OTHER 1.5418 -- --

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
1.75 48.2 99.4 0.0344 0.0431 -- 5.11 11270 11208 0.0 0.0 32.3
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)
1.75 1.85 96.8 0.2572 0.2657 3.75 5.11 1736

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 1.9 48.22 -- 0.0 -- 9990 983 87.21 -- 0.209 0.203 0.272 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 1.901 1.95 -- 32 297 0.243 0.277 -- 38.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.508
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.37
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.844
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.154
r_mcbond_it 0.883
r_scangle_it 3.42
r_nbtor_refined 0.308
r_dihedral_angle_1_deg 6.089
r_angle_refined_deg 1.435
r_scbond_it 2.267
r_gen_planes_refined 0.005
r_mcangle_it 1.395
r_dihedral_angle_3_deg 16.677
r_dihedral_angle_2_deg 33.87
r_nbd_refined 0.21
r_chiral_restr 0.099
r_symmetry_vdw_refined 0.206
r_symmetry_hbond_refined 0.228
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.246
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1063
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 79

Software

Software
Software Name Purpose
SAINT data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
PROTEUM PLUS data collection version: PLUS
APEX data reduction