9R40 | pdb_00009r40

HaloTag bound to compound MRC71

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	25% PEG 4000, 0.1 M Na MES pH 6.5, 0.2 M Mg Chloride.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.797	α = 90
b = 62.797	β = 90
c = 163.274	γ = 90

Symmetry
Space Group	P 43 21 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 X 16M		2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.04	58.68	99.7	1	4.8	10.1		21548

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	2.04	2.08			0.1

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	FREE R-VALUE	2.043	58.68	21479	1048	99.634	0.24	0.2373	0.233	0.2861	0.2831	38.043

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]
2.44			2.44		-4.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.724
r_dihedral_angle_6_deg	13.601
r_dihedral_angle_2_deg	8.83
r_dihedral_angle_1_deg	7.245
r_lrange_other	7.003
r_lrange_it	6.999
r_scangle_it	4.673
r_scangle_other	4.671
r_mcangle_other	4.366
r_mcangle_it	4.363
r_scbond_it	2.991
r_scbond_other	2.99
r_mcbond_other	2.957
r_mcbond_it	2.956
r_angle_refined_deg	1.613
r_angle_other_deg	0.547
r_symmetry_nbd_refined	0.29
r_nbd_refined	0.216
r_nbd_other	0.211
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.018
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2351
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing