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
FLAT PANEL 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_scangle_it 3.885
r_scbond_it 2.769
r_mcangle_it 1.55
r_mcbond_other 0.303
r_mcbond_it 1.363
r_nbd_refined 0.215
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.11
r_dihedral_angle_4_deg 15.453
r_dihedral_angle_3_deg 11.751
r_dihedral_angle_2_deg 32.25
r_dihedral_angle_1_deg 6.233
r_angle_other_deg 0.884
r_angle_refined_deg 1.567
r_bond_other_d 0.002
r_bond_refined_d 0.017
r_nbd_other 0.177
r_nbtor_refined 0.184
r_nbtor_other 0.102
r_xyhbond_nbd_refined 0.128
r_symmetry_vdw_refined 0.135
r_symmetry_vdw_other 0.225
r_symmetry_hbond_refined 0.116
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement
MOLREP model building
MAR345dtb data collection