X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 292.0
Details 0.1 M sodium citrate, 0.2 M ammonium acetate, 24% PEG 8000, 0.2 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.9 α = 90
b = 49.27 β = 98.38
c = 57.08 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
IMAGE PLATE MAR555 FLAT PANEL mirrors 2006-07-02
Diffraction Radiation
Monochromator Protocol
Ge(111) triangular bent crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81620 EMBL/DESY, Hamburg X11

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
1.68 30 99.0 0.069 -- -- 6.2 34231 34231 -- -3.0 24.6
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)
1.68 1.74 92.7 0.264 -- 5.1 4.8 3131

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 1.68 20.0 -3.0 -- 33126 33126 1076 99.04 0.1375 0.1375 0.1364 0.1713 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 1.68 1.723 2219 66 2219 0.157 0.204 -- 91.55
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 17.54
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.05
Anisotropic B[2][2] -0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.58
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 15.453
r_angle_refined_deg 1.567
r_dihedral_angle_2_deg 32.25
r_mcbond_it 1.363
r_mcangle_it 1.55
r_nbtor_refined 0.184
r_symmetry_hbond_refined 0.116
r_chiral_restr 0.11
r_dihedral_angle_1_deg 6.233
r_nbd_other 0.177
r_scbond_it 2.769
r_bond_other_d 0.002
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.128
r_gen_planes_refined 0.008
r_symmetry_vdw_refined 0.135
r_bond_refined_d 0.017
r_nbtor_other 0.102
r_scangle_it 3.885
r_symmetry_vdw_other 0.225
r_nbd_refined 0.215
r_mcbond_other 0.303
r_angle_other_deg 0.884
r_dihedral_angle_3_deg 11.751
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2509
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 338

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.2.0003
DENZO data reduction
SCALEPACK data scaling