2O2V

Crystal Structure of the Complex of Human Mitogen Activated Protein Kinase Kinase 5 Phox Domain (MAP2K5-phox) with Human Mitogen Activated Protein Kinase Kinase Kinase 3 (MAP3K3B-phox)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 277.0
Details 0.02M CaCl2, 0.1M Na(CH3COO), 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.65 α = 90
b = 87.65 β = 90
c = 55.41 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
IMAGE PLATE RIGAKU RAXIS -- 2006-11-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
1.83 50 99.3 0.075 0.075 -- 6.1 19661 19523 -- -- --
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)
1.83 1.9 96.5 0.578 0.578 -- 3.7 1836

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 1.83 46.83 -- 0.0 -- 19483 997 99.31 0.196 0.196 0.194 0.224 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 1.83 1.876 1345 67 1278 0.328 0.422 -- 95.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.491
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_nbd_refined 0.207
r_mcbond_it 1.005
r_mcangle_it 1.566
r_symmetry_vdw_refined 0.227
r_mcbond_other 0.259
r_scangle_it 3.552
r_nbtor_refined 0.167
r_nbtor_other 0.087
r_dihedral_angle_3_deg 12.093
r_nbd_other 0.199
r_chiral_restr 0.086
r_bond_other_d 0.001
r_dihedral_angle_4_deg 19.166
r_symmetry_vdw_other 0.231
r_dihedral_angle_1_deg 5.802
r_xyhbond_nbd_refined 0.122
r_symmetry_hbond_refined 0.155
r_gen_planes_refined 0.006
r_angle_other_deg 1.005
r_angle_refined_deg 1.577
r_dihedral_angle_2_deg 30.369
r_gen_planes_other 0.001
r_scbond_it 2.524
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1371
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 141

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
CrystalClear data collection version: (MSC/RIGAKU)
HKL-2000 data reduction
HKL-2000 data scaling