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_scangle_it 3.42
r_scbond_it 2.267
r_mcangle_it 1.395
r_mcbond_it 0.883
r_symmetry_hbond_refined 0.228
r_bond_refined_d 0.014
r_angle_refined_deg 1.435
r_dihedral_angle_1_deg 6.089
r_dihedral_angle_2_deg 33.87
r_dihedral_angle_3_deg 16.677
r_dihedral_angle_4_deg 19.844
r_chiral_restr 0.099
r_gen_planes_refined 0.005
r_nbd_refined 0.21
r_nbtor_refined 0.308
r_xyhbond_nbd_refined 0.154
r_symmetry_vdw_refined 0.206
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.246
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1043
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 71

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
APEXII Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 refinement
Phaser molecular replacement
SAINT data processing