2O63 | pdb_00002o63

Crystal structure of Pim1 with Myricetin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NA ACETATE, IMIDAZOLE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.711	α = 90
b = 98.711	β = 90
c = 80.596	γ = 120

Symmetry
Space Group	P 65

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	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.10000	ALS	8.3.1

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	84.51	99.79	0.129	5.1	5	28657	28657

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.052	99.8		0.702	2.3	4.9	4221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	84.51	28657	28657	1524	99.79	0.19445	0.19445	0.19322	0.21776	RANDOM	18.881

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]
1.55	0.77		1.55		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	3.049
r_scangle_it	2.452
r_scbond_it	1.418
r_angle_refined_deg	1.361
r_mcangle_it	1.098
r_angle_other_deg	0.823
r_mcbond_it	0.58
r_symmetry_vdw_refined	0.283
r_symmetry_vdw_other	0.263
r_nbd_other	0.24
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.087
r_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2230
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing