7EPG

Crystal structure of E.coli CcdB mutant S12G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VUB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.15 M CaCl2.2H2O, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.57	α = 90
b = 36.53	β = 93.691
c = 67.528	γ = 90

Symmetry
Space Group	I 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2019-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.5418

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	1.63	33.69	90.6	0.083	0.093	0.041	0.995	9.8	4.9		9822			11.66

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	1.63	1.72	86.9		0.195	0.218	0.097	0.967	4.8	4.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3VUB	1.631	33.69	9822	455	89.92	0.23	0.2276	0.23	0.2694	0.28	0	17.012

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]
-0.381		0.446	0.702		-0.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.127
r_dihedral_angle_4_deg	17.491
r_dihedral_angle_3_deg	14.173
r_dihedral_angle_1_deg	6.288
r_lrange_it	4.629
r_lrange_other	4.497
r_scangle_it	2.294
r_scangle_other	2.293
r_mcangle_it	2.263
r_mcangle_other	2.245
r_angle_refined_deg	1.484
r_mcbond_it	1.416
r_scbond_it	1.403
r_scbond_other	1.401
r_mcbond_other	1.385
r_angle_other_deg	1.253
r_symmetry_nbd_refined	0.266
r_nbd_other	0.256
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.183
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	792
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing