Experiment: 9F83

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CDZ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	50mM HEPES pH 6.8 150mM Sodium Chloride 24% PEG 3350 2% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.6

Symmetry
Space Group	P 1 21 1

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 X 16M		2023-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.7	84.55	98.9	0.078	0.093	0.049	0.998	12.1	6.6		59866

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	1.7	1.73			1.101	1.303	0.688	0.736		6.8

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	FREE R-VALUE	1.7	50.479	58347	2793	96.354	0.232	0.2291	0.2303	0.2802	0.2806	41.319

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]
-1.986		-0.312	0.731		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_other	42.511
r_scbond_it	42.49
r_scangle_it	38.383
r_scangle_other	38.377
r_lrange_other	34.911
r_mcbond_it	34.72
r_mcbond_other	34.72
r_lrange_it	34.447
r_mcangle_it	27.5
r_mcangle_other	27.495

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_other	42.511
r_scbond_it	42.49
r_scangle_it	38.383
r_scangle_other	38.377
r_lrange_other	34.911
r_mcbond_it	34.72
r_mcbond_other	34.72
r_lrange_it	34.447
r_mcangle_it	27.5
r_mcangle_other	27.495
r_dihedral_angle_6_deg	13.513
r_dihedral_angle_3_deg	12.57
r_dihedral_angle_2_deg	11.104
r_dihedral_angle_1_deg	7.936
r_angle_refined_deg	2.083
r_angle_other_deg	0.782
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.164
r_ncsr_local_group_4	0.138
r_ncsr_local_group_6	0.127
r_ncsr_local_group_2	0.122
r_nbd_other	0.121
r_ncsr_local_group_5	0.115
r_symmetry_nbd_refined	0.112
r_chiral_restr	0.11
r_ncsr_local_group_3	0.103
r_ncsr_local_group_1	0.087
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3794
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms