29MC | pdb_000029mc

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	29LI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.12 M Ethylene glycols: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 30% v/v Mix 1: 40% v/v PEG 500* MME; 20% w/v PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.76

Symmetry
Space Group	P 21 21 21

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		2022-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.88559	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	1.2	62.03	99.4	0.073	0.076	0.022	0.997	26.4	13		31058

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	1.2	1.22		99.8	0.147	0.152	0.04	0.995		13.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.2	35.87	29494	1509	99.28	0.15508	0.15361	0.1612	0.18167	0.1886	RANDOM	13.667

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]
0.77			-0.17		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.733
r_long_range_B_refined	11.509
r_long_range_B_other	11.28
r_dihedral_angle_2_deg	9.618
r_scangle_other	7.416
r_mcangle_it	5.771
r_mcangle_other	5.771
r_dihedral_angle_1_deg	5.565
r_scbond_it	5.095
r_scbond_other	5.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.733
r_long_range_B_refined	11.509
r_long_range_B_other	11.28
r_dihedral_angle_2_deg	9.618
r_scangle_other	7.416
r_mcangle_it	5.771
r_mcangle_other	5.771
r_dihedral_angle_1_deg	5.565
r_scbond_it	5.095
r_scbond_other	5.092
r_mcbond_it	3.998
r_mcbond_other	3.973
r_rigid_bond_restr	3.748
r_angle_refined_deg	2.076
r_angle_other_deg	0.772
r_chiral_restr	0.11
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	978
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	26

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.