X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.7
Temperature 298.0
Details reservoir: 2.2M AmmoniumSulfate, 0.1M cictric acid, pH4.7. protein: 7mg/ml Hdm2 in 50mM TRIS pH8.0, 200mM NaCl, 1mM TCEP, 10% glycerol. drop: 1ul reservoir + 1ul protein

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.75 α = 90
b = 55.75 β = 90
c = 107.32 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2009-02-13
Diffraction Radiation
Monochromator Protocol
SI 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.00001 SLS X10SA

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
1.67 20 99.9 0.047 -- 94.144 33.9 -- 12116 -- -- --
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)
1.67 1.73 100.0 0.34 -- 7.49 23.4 1346

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 1.67 20.0 -- 0.0 -- 11475 576 99.84 -- 0.2394 0.239 0.2467 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 1.67 1.713 -- 29 818 0.271 0.339 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.286
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.081
r_dihedral_angle_3_deg 15.118
r_dihedral_angle_2_deg 40.449
r_dihedral_angle_1_deg 4.825
r_angle_refined_deg 1.155
r_dihedral_angle_4_deg 9.644
r_bond_refined_d 0.009
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 743
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 62

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.5.0063
MOLREP phasing version: 9.4.09