X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 40% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.08 α = 90
b = 60.52 β = 93.06
c = 38.22 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
CCD BRUKER APEX II multi-layer optics 2007-06-20
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE 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
2 21.88 100.0 0.0761 0.0364 -- 13.42 9648 9646 -- -- 34.2
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)
2.0 2.1 100.0 0.4489 0.3477 2.8 6.29 1307

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 2.0 21.88 -- 0.0 9617 8525 853 88.65 0.211 0.216 0.211 0.261 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 2.0 2.052 455 46 455 0.324 0.374 -- 72.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.683
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.02
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.217
r_dihedral_angle_3_deg 15.809
r_dihedral_angle_1_deg 6.148
r_symmetry_vdw_refined 0.169
r_xyhbond_nbd_refined 0.178
r_scangle_it 3.336
r_chiral_restr 0.11
r_symmetry_hbond_refined 0.177
r_nbtor_refined 0.308
r_angle_refined_deg 1.914
r_bond_refined_d 0.015
r_gen_planes_refined 0.005
r_mcangle_it 1.497
r_dihedral_angle_2_deg 36.912
r_dihedral_angle_4_deg 17.661
r_scbond_it 2.157
r_mcbond_it 0.912
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1041
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 54

Software

Software
Software Name Purpose
SAINT data scaling version: V7.34A
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
APEX data collection
SAINT data reduction