5QHA

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102951

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.8	α = 90
b = 123.8	β = 90
c = 41.06	γ = 120

Symmetry
Space Group	P 3 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 PILATUS 6M		2017-09-07		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.57	53.61	99.3	0.122	0.129	0.043	0.997	8.2	7.7		50185

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	1.57	1.61	97.5		2.865	3.147	1.28	0.534		5.8	3598

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5T3P	1.57	107.21	47257	2425	98.2	0.196	0.194	0.233	RANDOM	30.8

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]
-1.63	-0.82		-1.63		5.3

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	45.604
r_dihedral_angle_2_deg	29.918
r_sphericity_bonded	22.817
r_dihedral_angle_4_deg	16.049
r_dihedral_angle_3_deg	13.121
r_dihedral_angle_1_deg	6.297
r_mcangle_it	5.753
r_mcbond_it	4.727
r_mcbond_other	4.724
r_rigid_bond_restr	2.779
r_angle_refined_deg	1.813
r_angle_other_deg	1.057
r_chiral_restr	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
MAIN-CHAIN ANGLE OTHER ATOMS (A**2)
r_scbond_it
SIDE-CHAIN BOND OTHER ATOMS (A**2)
r_scangle_it
SIDE-CHAIN ANGLE OTHER ATOMS (A**2)
LONG RANGE B REFINED ATOMS (A**2)
LONG RANGE B OTHER ATOMS (A**2)

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1449
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing