8BL9 | pdb_00008bl9

Crystal Structure of Sam0.7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	20% w/v PEG3350, 200 mM KSCN

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.554	α = 90
b = 40.554	β = 90
c = 253.117	γ = 120

Symmetry
Space Group	P 65 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 EIGER2 X 16M		2021-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

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	1.8	35.12	100	0.103	0.999	19	32.77		12505

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	1.8	1.91	99.9		1.623	0.965	1.65	34.94

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	computational model	1.8	35.12	12505	626	99.984	0.259	0.2571	0.26	0.2961	0.31	49.962

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]
1.573	0.787		1.573		-5.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.92
r_dihedral_angle_4_deg	19.291
r_dihedral_angle_3_deg	17.273
r_dihedral_angle_1_deg	6.615
r_lrange_it	5.337
r_lrange_other	5.335
r_scangle_it	3.873
r_scangle_other	3.87
r_scbond_it	2.596
r_scbond_other	2.593
r_mcangle_it	2.561
r_mcangle_other	2.559
r_angle_refined_deg	1.959
r_mcbond_other	1.857
r_mcbond_it	1.855
r_angle_other_deg	1.332
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.136
r_nbd_other	0.131
r_symmetry_xyhbond_nbd_refined	0.093
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.023
r_gen_planes_refined	0.015
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	921
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

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