7V4S | pdb_00007v4s

Horcolin complex with methyl-alpha-mannose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.84	α = 90
b = 42.84	β = 90
c = 139.201	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS3 6M		2019-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	46.4	97.3	0.128	0.038	0.99	10.5	12		45978			11.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.26	95		0.98	0.289	0.77	2.3	12

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	THROUGHOUT	1X1V	1.2	37.128	45952	2326	96.761	0.211	0.2094	0.22	0.2346	0.23	13.729

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]
0.169	0.084		0.169		-0.547

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.684
r_dihedral_angle_4_deg	24.444
r_dihedral_angle_3_deg	11.672
r_dihedral_angle_1_deg	6.754
r_lrange_it	5.188
r_lrange_other	4.455
r_scangle_it	3.259
r_scangle_other	3.257
r_angle_other_deg	2.436
r_scbond_it	2.153
r_scbond_other	2.151
r_mcangle_other	2.009
r_mcangle_it	2.008
r_angle_refined_deg	1.981
r_mcbond_it	1.316
r_mcbond_other	1.301
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_other	0.176
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.166
r_nbd_refined	0.151
r_symmetry_nbtor_other	0.111
r_symmetry_nbd_refined	0.095
r_chiral_restr	0.092
r_bond_other_d	0.036
r_bond_refined_d	0.016
r_gen_planes_other	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1039
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	26

Software

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