7BK7 | pdb_00007bk7

PfCopC mutant - D83N

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	2.9 M ammonium sulphate, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.3	α = 90
b = 80.3	β = 90
c = 89.89	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 X 2M		2020-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.3	50	99.8	0.102	0.998	10.52	5.64		12725

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36			1.962	0.457

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6NFQ	2.3	35.266	12715	647	99.882	0.212	0.2082	0.21	0.2676	0.27	70.442

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]
-0.533			-0.533		1.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.75
r_dihedral_angle_3_deg	20.395
r_lrange_it	14.08
r_lrange_other	14.043
r_dihedral_angle_4_deg	14.008
r_scangle_it	9.492
r_scangle_other	9.483
r_mcangle_other	9.288
r_mcangle_it	9.287
r_dihedral_angle_1_deg	8.17
r_scbond_it	6.31
r_scbond_other	6.276
r_mcbond_it	6.217
r_mcbond_other	6.215
r_angle_refined_deg	1.561
r_angle_other_deg	1.22
r_nbd_other	0.292
r_symmetry_xyhbond_nbd_refined	0.253
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.205
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.063
r_symmetry_metal_ion_refined	0.012
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1398
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	17

Software

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