7ZC0 | pdb_00007zc0

4,6-alpha-glucanotransferase GtfC from Geobacillus 12AMOR1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BC9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.07-1.14 M (NH4)2SO4, 0.1 M MES-NaOH, pH 6.5, 0.4 M Na3Citrate

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 262.563	α = 90
b = 262.563	β = 90
c = 72.232	γ = 90

Symmetry
Space Group	I 41 2 2

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 EIGER2 XE 16M		2020-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.98006	Diamond	I03

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	2.25	131.28	99.3	0.999	20.5	1.9		59408

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	2.25	2.31	95		0.795	4.2	1.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3BC9	2.25	131.28	56439	2978	99.263	0.254	0.252	0.25	0.2925	0.29	54.197

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]
-0.256			-0.256		0.512

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.348
r_dihedral_angle_4_deg	19.444
r_dihedral_angle_3_deg	17.325
r_dihedral_angle_1_deg	7.758
r_lrange_it	3.968
r_angle_refined_deg	1.382
r_mcangle_it	0.699
r_scangle_it	0.573
r_mcbond_it	0.38
r_scbond_it	0.367
r_nbtor_refined	0.307
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.168
r_metal_ion_refined	0.098
r_chiral_restr	0.094
r_symmetry_xyhbond_nbd_refined	0.086
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5667
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	25

Software

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