7BK6

PfCopC mutant - D83A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NFQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	2.5 M ammonium sulphate, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.06	α = 90
b = 80.06	β = 90
c = 89.4	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2020-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.15	44.7	100	1	18.69	13.7		15379

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	99.7		0.544		13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6NFQ	2.15	40.062	15378	787	99.955	0.217	0.2147	0.2634	67.356

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]
0.153			0.153		-0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.677
r_dihedral_angle_4_deg	27.328
r_dihedral_angle_3_deg	18.742
r_lrange_other	12.182
r_lrange_it	12.162
r_dihedral_angle_1_deg	9.217
r_scangle_it	8.885
r_scangle_other	8.852
r_mcangle_it	8.825
r_mcangle_other	8.825
r_mcbond_other	6.526
r_mcbond_it	6.518
r_scbond_it	6.067
r_scbond_other	5.985
r_angle_refined_deg	1.644
r_angle_other_deg	1.278
r_symmetry_nbd_refined	0.327
r_symmetry_xyhbond_nbd_refined	0.301
r_nbd_other	0.294
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.227
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.161
r_metal_ion_refined	0.156
r_symmetry_metal_ion_refined	0.147
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1396
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing