3HU2 | pdb_00003hu2

Structure of p97 N-D1 R86A mutant in complex with ATPgS

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	288	100mM NaCl, 4% benzamidine, 100mM citrate, pH 5.8, 16.5% PEG3350 and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.892	α = 97.52
b = 102.645	β = 90.63
c = 107.182	γ = 91.45

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.85	40		0.049	13.8			85163

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.85	40	79168	4194	93.01	0.25936	0.25773	0.23	0.29027	0.26	RANDOM	70.682

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]
3.47	-0.14	0.9	-0.62	-2.48	-3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.298
r_dihedral_angle_3_deg	19.527
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_1_deg	6.074
r_scangle_it	1.646
r_angle_refined_deg	1.52
r_scbond_it	1.124
r_mcangle_it	0.65
r_mcbond_it	0.433
r_symmetry_hbond_refined	0.325
r_nbtor_refined	0.264
r_symmetry_vdw_refined	0.222
r_metal_ion_refined	0.211
r_nbd_refined	0.161
r_chiral_restr	0.127
r_xyhbond_nbd_refined	0.107
r_bond_refined_d	0.02
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21168
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	192

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling