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_symmetry_hbond_refined 0.084
r_angle_other_deg 3.966
r_symmetry_vdw_refined 0.079
r_gen_planes_refined 0.007
r_nbd_refined 0.192
r_dihedral_angle_3_deg 15.063
r_bond_other_d 0.0
r_dihedral_angle_1_deg 6.16
r_dihedral_angle_2_deg 38.254
r_xyhbond_nbd_refined 0.137
r_nbtor_refined 0.181
r_symmetry_vdw_other 0.38
r_gen_planes_other 0.007
r_dihedral_angle_4_deg 15.209
r_nbd_other 0.232
r_angle_refined_deg 1.253
r_bond_refined_d 0.01
r_nbtor_other 0.108
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

Software
Software Name Purpose
ADSC data collection version: Quantum
MOLREP phasing
CHAINSAW model building
REFMAC refinement
ARP/wARP model building
MOSFLM data reduction
SCALA data scaling
CHAINSAW phasing
REFMAC phasing