X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.17 α = 90
b = 153.49 β = 104.25
c = 100.66 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 ADSC mirrors --
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97925 NSLS X4A

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
2.5 50 96.2 0.122 0.122 -- 7.2 86579 86579 -- -- --
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)
2.5 2.6 80.8 0.324 0.32 3.2 6.0 7232

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 2.55 50.0 -- 0.0 -- 86551 4338 96.16 -- 0.217 0.214 0.252 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 2.55 2.618 -- 259 4935 0.271 0.35 -- 78.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.947
Anisotropic B[1][1] 2.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.8
Anisotropic B[2][2] -1.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.43
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.314
r_scbond_it 2.196
r_dihedral_angle_1_deg 7.726
r_xyhbond_nbd_refined 0.156
r_symmetry_vdw_refined 0.152
r_bond_refined_d 0.016
r_chiral_restr 0.122
r_scangle_it 3.586
r_nbd_refined 0.232
r_gen_planes_refined 0.006
r_angle_refined_deg 1.765
r_mcangle_it 1.474
r_dihedral_angle_2_deg 39.861
r_symmetry_hbond_refined 0.094
r_dihedral_angle_4_deg 17.424
r_dihedral_angle_3_deg 19.427
r_mcbond_it 0.877
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14377
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 488

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.004