2VMT

Crystal structure of Y60AbsSHMT L-Ser external aldimine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KL1	PDB ENTRY 1KL1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		50% MPD, 0.1 M HEPES PH 7.5, 0.2 MM EDTA, 5 MM 2-MERCAPTOETHANOL, 10 MM L-SER

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.275	α = 90
b = 106.584	β = 90
c = 57.274	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	OSMIC MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.66	30	89.6	0.03	40.6	6.4		39211			18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.72	73.1		0.19	8	5.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1KL1	1.72	23.2	35295	1840	91.4	0.183	0.182	0.212	RANDOM	14.44

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]
-0.01			-0.03		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.296
r_dihedral_angle_4_deg	15.068
r_dihedral_angle_3_deg	12.512
r_dihedral_angle_1_deg	5.126
r_scangle_it	1.895
r_scbond_it	1.163
r_angle_refined_deg	1.056
r_mcangle_it	0.624
r_mcbond_it	0.379
r_nbtor_refined	0.301
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.156
r_symmetry_hbond_refined	0.102
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3109
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing