7QQF | pdb_00007qqf

Crystal structure of unliganded MYORG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F2H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	100 mM HEPES pH 7.0, 10% PEG MME5000 and 5% tasimate pH 7.0.

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.109	α = 88.062
b = 78.986	β = 78.801
c = 180.113	γ = 62.714

Symmetry
Space Group	P 1

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 XE 16M		2019-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97951	Diamond	I04

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	2.43	66.57	98.2	0.066	0.093	0.066	0.983	8.2	2.2		131515

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	2.43	2.47			1.071	1.514	1.071	0.515	1	2.1

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	THROUGHOUT	2F2H	2.43	66.57	131476	6445	98.149	0.212	0.2108	0.21	0.233	0.23	58.353

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]
-0.158	0.096	-1.604	1.904	0.501	-3.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.627
r_dihedral_angle_4_deg	17.561
r_dihedral_angle_3_deg	16.065
r_dihedral_angle_1_deg	7.035
r_lrange_it	3.972
r_lrange_other	3.966
r_scangle_it	1.54
r_scangle_other	1.54
r_mcangle_it	1.53
r_mcangle_other	1.53
r_angle_refined_deg	1.377
r_angle_other_deg	1.139
r_mcbond_it	0.908
r_mcbond_other	0.908
r_scbond_it	0.908
r_scbond_other	0.908
r_nbd_other	0.245
r_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.177
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.151
r_xyhbond_nbd_refined	0.142
r_ncsr_local_group_3	0.092
r_ncsr_local_group_5	0.092
r_ncsr_local_group_6	0.085
r_ncsr_local_group_4	0.078
r_ncsr_local_group_2	0.077
r_ncsr_local_group_1	0.076
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.055
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19386
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	531

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing