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, 0.4 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.31 α = 90
b = 49.2 β = 98.84
c = 57.43 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 2007-02-04
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 0.81480 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
1.55 40 100.0 0.091 -- -- 3.8 44391 44391 -- -3.0 21.2
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)
1.55 1.61 100.0 0.68 -- 2.1 3.8 4390

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 1.55 20.0 -3.0 -- 43213 43213 1139 99.91 0.1515 0.1515 0.1507 0.1806 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 1.55 1.59 3125 95 3125 0.199 0.286 -- 99.26
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 15.27
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.47
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.35
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.47
r_dihedral_angle_3_deg 11.925
r_bond_other_d 0.001
r_xyhbond_nbd_refined 0.121
r_angle_other_deg 0.887
r_nbtor_refined 0.19
r_symmetry_hbond_refined 0.125
r_dihedral_angle_4_deg 15.502
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 32.661
r_nbd_refined 0.218
r_nbd_other 0.173
r_symmetry_vdw_other 0.195
r_mcbond_it 1.051
r_chiral_restr 0.11
r_dihedral_angle_1_deg 6.2
r_symmetry_vdw_refined 0.134
r_gen_planes_refined 0.009
r_nbtor_other 0.088
r_scangle_it 3.674
r_angle_refined_deg 1.644
r_gen_planes_other 0.001
r_mcbond_other 0.32
r_mcangle_it 1.592
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2509
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 356

Software

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