9HQT | pdb_00009hqt

SFX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HIH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE291Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4.
Crystal Properties
Matthews coefficientSolvent content
2.9563.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.1α = 90
b = 107.1β = 90
c = 107.1γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDMPCCD2019-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.127SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlDetails Sample Solvent
1Oxford silicon chipsGeobrick and Smaract
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
110 (fs)302.5611 (KeV)
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.833.891000.9380.2044233.738160
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.6390.4922.1159.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.833.8938147188699.9450.1910.190.190.2190.219129.718
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.031
r_dihedral_angle_3_deg12.124
r_lrange_it7.434
r_lrange_other7.401
r_dihedral_angle_1_deg6.846
r_dihedral_angle_2_deg6.572
r_scangle_it4.825
r_scangle_other4.823
r_scbond_other3.124
r_scbond_it3.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.031
r_dihedral_angle_3_deg12.124
r_lrange_it7.434
r_lrange_other7.401
r_dihedral_angle_1_deg6.846
r_dihedral_angle_2_deg6.572
r_scangle_it4.825
r_scangle_other4.823
r_scbond_other3.124
r_scbond_it3.123
r_angle_refined_deg2.317
r_mcangle_other2.309
r_mcangle_it2.307
r_mcbond_it1.611
r_mcbond_other1.611
r_angle_other_deg0.628
r_nbd_refined0.204
r_symmetry_nbd_other0.201
r_nbd_other0.195
r_nbtor_refined0.182
r_symmetry_nbd_refined0.182
r_symmetry_xyhbond_nbd_refined0.124
r_xyhbond_nbd_refined0.121
r_symmetry_nbtor_other0.088
r_chiral_restr0.087
r_bond_refined_d0.017
r_gen_planes_other0.014
r_gen_planes_refined0.013
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2126
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms105

Software

Software
Software NamePurpose
CrystFELdata reduction
PRIMEdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building