9D9I | pdb_00009d9i

Human Hsp90b nucleotide binding domain in complex with BRI2312

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NMQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	21% PEG6000, 0.1M NaCacodylate pH 6.6, 1M Li

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.794	α = 90
b = 90.524	β = 90
c = 97.451	γ = 90

Symmetry
Space Group	I 2 2 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 EIGER R 1M		2021-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU MICROMAX-003	1.54189

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	1.5	29.21	98.2	0.047	0.052	0.021	0.999	15.5	4.9		46661

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	1.5	1.53		87.7	0.582	0.704	0.385	0.733		2.8

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	THROUGHOUT	1.5	28.841	45618	2286	95.854	0.16	0.159	0.1601	0.1868	0.1881	20.78

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]
-0.895			0.319		0.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.264
r_dihedral_angle_3_deg	11.793
r_dihedral_angle_2_deg	8.397
r_lrange_it	6.936
r_lrange_other	6.392
r_dihedral_angle_1_deg	6.382
r_scangle_it	4.981
r_scangle_other	4.979
r_scbond_it	3.173
r_scbond_other	3.17
r_mcangle_other	2.829
r_mcangle_it	2.822
r_angle_refined_deg	2.011
r_mcbond_other	1.81
r_mcbond_it	1.809
r_angle_other_deg	0.834
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.176
r_symmetry_nbd_other	0.17
r_nbd_other	0.115
r_symmetry_xyhbond_nbd_refined	0.11
r_chiral_restr	0.096
r_symmetry_nbd_refined	0.083
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1645
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
PHASER	phasing