X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 277.0
Details 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.16 α = 90
b = 60 β = 95.06
c = 38.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification 2011-09-25
Diffraction Radiation
Monochromator Protocol
Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25

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
1.65 50 99.9 0.042 -- -- 6.4 17188 17188 0.0 0.0 28.5
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)
1.65 1.68 99.4 0.135 -- -- 5.8 836

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 1.65 38.73 -- 0.0 17170 17170 869 99.72 -- 0.1803 0.1785 0.2175 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 1.65 1.693 1203 55 1148 0.255 0.282 -- 97.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.1209
Anisotropic B[1][1] -1.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.7
Anisotropic B[2][2] -1.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.43
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.014
r_chiral_restr 0.141
r_dihedral_angle_4_deg 11.792
r_dihedral_angle_3_deg 15.062
r_dihedral_angle_2_deg 34.428
r_dihedral_angle_1_deg 6.292
r_angle_refined_deg 1.982
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1024
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 131

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement
SCALEPACK data reduction