9QVR | pdb_00009qvr

Crystal structure of the CtaG_H128A variant from Ruminiclostridium cellulolyticum in complex with PHBA (P2(1)2(1)2(1)-medium)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9QUZ	Crystal structure of CtaG from Ruminiclostridium cellulolyticum (P2(1)-small)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M Ammoniumphosphate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.69	α = 90
b = 99.67	β = 90
c = 100.74	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 EIGER X 16M		2020-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	30	97.4	0.067	18	6.1		65109

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8	99.7		0.651	3.7	6.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	30	61844	3255	97.41	0.20406	0.20265	0.2108	0.22936	0.2396	RANDOM	20.743

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]
-0.32			1.15		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.126
r_dihedral_angle_4_deg	19.516
r_dihedral_angle_3_deg	13.832
r_dihedral_angle_1_deg	6.564
r_long_range_B_refined	2.384
r_long_range_B_other	2.324
r_scangle_other	1.636
r_mcangle_it	1.537
r_mcangle_other	1.537
r_angle_other_deg	1.227
r_scbond_it	1.218
r_scbond_other	1.218
r_angle_refined_deg	1.186
r_mcbond_it	1.132
r_mcbond_other	1.132
r_rigid_bond_restr	0.523
r_chiral_restr	0.056
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5126
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing