X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4
Temperature 290.0
Details 0.1M Na Citrate, pH 4.0, 0.1M Potassium Phosphate Mono-Basic, 50% PEG1000, Micro-batch, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.18 α = 90
b = 35.8 β = 107.02
c = 118.03 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2005-12-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.9 15 96.0 0.08 0.08 -- 3.3 37592 37592 0.0 0.0 --
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 2.0 95.1 0.324 0.324 1.9 3.1 5405

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 15.0 -- 0.0 37592 37592 1890 95.43 0.201 0.201 0.199 0.234 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 1.9 1.949 2677 140 2537 0.26 0.306 -- 94.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.876
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.26
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.178
r_mcangle_it 1.163
r_bond_other_d 0.001
r_scangle_it 2.914
r_dihedral_angle_4_deg 14.545
r_nbtor_other 0.084
r_mcbond_it 0.799
r_dihedral_angle_3_deg 12.419
r_angle_refined_deg 1.221
r_nbd_other 0.181
r_angle_other_deg 0.928
r_nbtor_refined 0.165
r_symmetry_vdw_other 0.196
r_mcbond_other 0.156
r_symmetry_vdw_refined 0.223
r_dihedral_angle_1_deg 6.048
r_scbond_it 1.978
r_chiral_restr 0.126
r_gen_planes_refined 0.004
r_gen_planes_other 0.002
r_nbd_refined 0.211
r_bond_refined_d 0.011
r_dihedral_angle_2_deg 39.348
r_xyhbond_nbd_refined 0.148
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4265
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 346

Software

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection
XDS data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing