8RVK | pdb_00008rvk

Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L5V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2-0.5 M Li2SO4 monohydrate, 0.1 M Bis-Tris pH 5.5-7.0 and 25-30% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.498	α = 90
b = 119.79	β = 90
c = 150.75	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		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.89	71.503	99.9	0.992	5.9	1.9		160021

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	1.89	1.92	97.1		0.284	0.3

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	NONE	2.18	71.503	159923	1377	99.992	0.178	0.1773	0.19	0.2294	0.24	36.046

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]
2.095			-1.845		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.369
r_dihedral_angle_6_deg	15.704
r_dihedral_angle_2_deg	12.402
r_lrange_other	8.268
r_lrange_it	8.266
r_scangle_it	7.713
r_scangle_other	7.395
r_dihedral_angle_1_deg	7.25
r_scbond_it	5.817
r_mcangle_other	5.743
r_mcangle_it	5.741
r_scbond_other	5.617
r_mcbond_it	4.589
r_mcbond_other	4.583
r_angle_refined_deg	2.381
r_angle_other_deg	0.842
r_symmetry_xyhbond_nbd_refined	0.288
r_nbd_refined	0.232
r_nbd_other	0.228
r_symmetry_nbd_other	0.206
r_symmetry_nbd_refined	0.202
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.132
r_symmetry_xyhbond_nbd_other	0.095
r_ncsr_local_group_1	0.095
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12599
Nucleic Acid Atoms
Solvent Atoms	630
Heterogen Atoms	312

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
Coot	model building
MOLREP	phasing
xia2	data reduction