7VG5 | pdb_00007vg5

10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1 with tetrahydrofolate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	PEG 3350, magnesium chloride hexahydrate, BIS-TRIS

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.322	α = 90
b = 49.513	β = 97.38
c = 64.071	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	CCD	ADSC QUANTUM 270		2020-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.25	50	97.7	0.119	0.142	0.077	14.3	3		18336

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	2.25	2.29	96.1		0.308	0.382	0.223	0.656		2.5

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 (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	1O5H	2.25	31.79	17433	903	97.61	0.1936	0.1902	0.2	0.2572	0.26	RANDOM	33.91

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]
-1.45		-0.45	-0.33		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.567
r_dihedral_angle_3_deg	15.485
r_dihedral_angle_4_deg	13.789
r_dihedral_angle_1_deg	5.188
r_angle_refined_deg	1.481
r_angle_other_deg	1.377
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.567
r_dihedral_angle_3_deg	15.485
r_dihedral_angle_4_deg	13.789
r_dihedral_angle_1_deg	5.188
r_angle_refined_deg	1.481
r_angle_other_deg	1.377
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2984
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	26

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

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.