6GPR | pdb_00006gpr

Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) in complex with cAMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5 Sample: Hsp90a-NTD 20 mg/mL, 10 mM cAMP, 500 mM NaCl, 20 mM TRIS, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.502	α = 90
b = 44.346	β = 115.6
c = 54.023	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2018-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

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	2.35	48.72	99.8	0.144	0.17	0.089	0.962	6.6	3.7		9680		2	14.3

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	2.35	2.48	99.7		0.34	0.398	0.205	0.874	3.9	3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2XK2	2.35	48.72	9135	515	99.57	0.22639	0.22317	0.23	0.2858	0.3	RANDOM	21.603

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]
1.65		-4.47	11.06		-5.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.048
r_dihedral_angle_4_deg	28.278
r_dihedral_angle_3_deg	17.845
r_dihedral_angle_1_deg	8.393
r_long_range_B_refined	4.68
r_mcangle_it	2.337
r_angle_refined_deg	1.771
r_scbond_it	1.708
r_mcbond_it	1.498
r_chiral_restr	0.171
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1642
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing