8Y9R | pdb_00008y9r

Crystal structure of Spiral2 microtubule-binding domain from Physcomitrella patens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M sodium citrate (pH 5.0), 0.2 M NaH2SO4, 50 mM guanidine hydrochloride and 1.4 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.826	α = 90
b = 95.646	β = 90
c = 150.018	γ = 90

Symmetry
Space Group	P 2 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		2021-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.97899	Photon Factory	BL-5A

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	2.7	48.11	99.6	0.15	0.163	0.063	0.998	10	6.6		24426

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83			1.593	0.673	0.693		6.5

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	SAD	FREE R-VALUE	2.799	48.095	21924	1107	99.909	0.218	0.2149	0.2234	0.2764	0.2787	59.541

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]
-1.366			4.995		-3.628

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.995
r_dihedral_angle_6_deg	16.31
r_dihedral_angle_2_deg	16.162
r_lrange_it	13.867
r_lrange_other	13.866
r_scangle_it	10.762
r_scangle_other	10.76
r_mcangle_other	10.022
r_mcangle_it	10.02
r_dihedral_angle_1_deg	7.747
r_scbond_it	7.148
r_scbond_other	7.146
r_mcbond_it	6.809
r_mcbond_other	6.809
r_angle_refined_deg	1.856
r_angle_other_deg	0.623
r_nbd_other	0.275
r_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.238
r_symmetry_nbd_refined	0.23
r_xyhbond_nbd_refined	0.223
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.184
r_ncsr_local_group_1	0.105
r_symmetry_xyhbond_nbd_other	0.096
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4222
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
CRANK2	phasing