6HPQ | pdb_00006hpq

Crystal structure of human Pif1 helicase in complex with AMP-PNP, brominated crystal form.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Na-acetate, PEG 2K MME, Tris-Cl

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.25	α = 90
b = 76.82	β = 90
c = 142.54	γ = 90

Symmetry
Space Group	P 21 21 21

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 S 6M		2015-10-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.91966, 0.91992, 0.91912	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.43	73.25	99.9	0.146	0.999	9.6	12.8		148682			20.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.47	99.8		2.316	0.598		10.7

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		THROUGHOUT	1.43	71.37	141225	7357	99.89	0.22579	0.22366	0.22	0.26633	0.27	RANDOM	18.412

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]
-0.37					0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.992
r_dihedral_angle_2_deg	31.815
r_dihedral_angle_4_deg	22.61
r_sphericity_bonded	18.391
r_dihedral_angle_3_deg	15.092
r_long_range_B_refined	6.347
r_dihedral_angle_1_deg	6.23
r_long_range_B_other	5.081
r_scangle_other	4.865
r_scbond_it	4.186
r_scbond_other	4.186
r_mcangle_other	3.547
r_mcangle_it	3.54
r_rigid_bond_restr	3.158
r_mcbond_it	2.73
r_mcbond_other	2.711
r_angle_refined_deg	1.958
r_angle_other_deg	1.573
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	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
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6338
Nucleic Acid Atoms
Solvent Atoms	1197
Heterogen Atoms	73

Software

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