X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 294.0
Details 10% PEG 3350, 150 mM NaCl, 50 mM sodium. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.95 α = 90
b = 83.95 β = 90
c = 173.84 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 BENT MIRRORS 2010-12-05
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 -- DIAMOND I02

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
2.15 40 99.3 0.078 0.078 -- 3.9 34324 34324 -- -- 33.4
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)
2.15 2.27 99.9 0.31 0.31 2.5 4.0 4957

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 2.15 38.6 -- -- 34274 34274 1729 98.96 0.17832 0.17832 0.17632 0.21631 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 2.15 2.206 2486 138 2348 0.203 0.288 -- 99.92
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.192
r_gen_planes_other 0.007
r_gen_planes_refined 0.007
r_dihedral_angle_4_deg 15.209
r_dihedral_angle_3_deg 15.063
r_dihedral_angle_2_deg 38.254
r_dihedral_angle_1_deg 6.16
r_angle_other_deg 3.966
r_angle_refined_deg 1.253
r_bond_other_d 0.0
r_bond_refined_d 0.01
r_nbd_other 0.232
r_nbtor_refined 0.181
r_nbtor_other 0.108
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.079
r_symmetry_vdw_other 0.38
r_symmetry_hbond_refined 0.084
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3199
Nucleic Acid Atoms 570
Heterogen Atoms 32
Solvent Atoms 267

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP, CHAINSAW, REFMAC, ARP/WARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
ARP/WARP model building
REFMAC model building
CHAINSAW model building
MOLREP model building
ADSC version: Quantum data collection