7MXZ | pdb_00007mxz

Sy-CrtE apo structure

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KRO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Droplets were 200 nL protein at 10 mg/mL plus 200 nL reservoir, 0.2 M MgCl2 and 20 %(w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.497	α = 90
b = 73.65	β = 95.675
c = 132.172	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2020-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.47	43.84	98.2	0.085	0.035	0.999	10.5	6.9		98723

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	1.47	1.49	89.6		0.805	0.334	0.885		6.6

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	3kro	1.47	39.763	98635	4987	98.148	0.162	0.1604	0.16	0.1847	0.19	18.078

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]
1.868		0.121	-1.377		-0.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.191
r_dihedral_angle_4_deg	21.638
r_dihedral_angle_3_deg	12.342
r_lrange_it	5.736
r_lrange_other	5.658
r_scangle_it	4.741
r_scangle_other	4.74
r_dihedral_angle_1_deg	4.537
r_scbond_it	3.079
r_scbond_other	3.078
r_mcangle_it	2.512
r_mcangle_other	2.512
r_angle_refined_deg	1.844
r_mcbond_it	1.718
r_mcbond_other	1.716
r_angle_other_deg	1.623
r_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.202
r_nbd_other	0.179
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.166
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.136
r_chiral_restr	0.102
r_symmetry_xyhbond_nbd_other	0.101
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4313
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	5

Software

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