9DKS | pdb_00009dks

Crystal structure of CcbD C19S mutant complexed with single PCP domain of CcbZ

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DKR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.2 M sodium malonate, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.28	α = 90
b = 89.079	β = 90
c = 135.029	γ = 90

Symmetry
Space Group	P 21 21 21

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 S 6M		2022-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11588	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.55	135.03	100	0.076	0.083	0.032	1	18.7	13		132094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	100		1.973	2.141	0.826	0.649	1.5	12.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.55	74.467	131999	6716	99.988	0.178	0.1769	0.1766	0.2051	0.2047	25.25

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]
2.254			-1.342		-0.912

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.87
r_dihedral_angle_4_deg	17.298
r_dihedral_angle_3_deg	12.714
r_lrange_it	6.062
r_dihedral_angle_1_deg	5.983
r_lrange_other	5.972
r_scangle_it	4.828
r_scangle_other	4.827
r_scbond_it	3.301
r_scbond_other	3.301
r_mcangle_it	2.962
r_mcangle_other	2.962
r_mcbond_it	2.143
r_mcbond_other	2.143
r_angle_refined_deg	1.674
r_angle_other_deg	1.546
r_nbd_refined	0.215
r_nbd_other	0.192
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.137
r_chiral_restr	0.091
r_symmetry_nbd_refined	0.085
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5949
Nucleic Acid Atoms
Solvent Atoms	660
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing