7NSZ | pdb_00007nsz

Drosophila PGRP-LB Y78F mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.69	27.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.502	α = 90
b = 40.502	β = 90
c = 338.941	γ = 120

Symmetry
Space Group	P 61 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		2019-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

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	1.3	338.94	99.9	0.096	0.098	0.022	0.998	20.8	31.5		42802

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	1.3	1.32			0.443	0.478	0.176	0.955		13

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	1OHT	1.3	56.554	42582	2133	99.939	0.188	0.1864	0.2	0.2207	0.23	13.906

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]
0.147	0.073		0.147		-0.476

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.19
r_dihedral_angle_4_deg	15.455
r_dihedral_angle_3_deg	10.466
r_dihedral_angle_1_deg	7.009
r_lrange_it	4.116
r_lrange_other	4.115
r_scangle_it	3.098
r_scangle_other	3.096
r_scbond_it	2.099
r_scbond_other	2.099
r_angle_refined_deg	1.904
r_mcangle_it	1.868
r_mcangle_other	1.861
r_angle_other_deg	1.524
r_mcbond_it	1.288
r_mcbond_other	1.277
r_nbd_other	0.26
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.22
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.131
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.085
r_symmetry_metal_ion_refined	0.063
r_bond_refined_d	0.014
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	1337
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data reduction
DIALS	data processing
Coot	model building
GDA	data collection
Aimless	data scaling
PHASER	phasing