7D27 | pdb_00007d27

Structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BUB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	21%(v/v) 2-propanl, 30% (v/v) Glyceol 0.07M sodium cacodylate trihydrate pH 6.5, 0.14M Sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
4	69.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.96	α = 90
b = 119.96	β = 90
c = 116.73	γ = 90

Symmetry
Space Group	P 42 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	104.15	PIXEL	DECTRIS EIGER X 9M		2020-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97949	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.48	29.18	100	0.023	20.4	17.7		30793

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.48	2.57			0.424

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	4BUB	2.48	20.001	30729	1983	99.727	0.23	0.2281	0.23	0.2598	0.26	28.554

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]
-0.002			-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.061
r_dihedral_angle_4_deg	18.792
r_dihedral_angle_3_deg	16.068
r_lrange_it	6.481
r_lrange_other	6.48
r_dihedral_angle_1_deg	6.25
r_scangle_it	6.038
r_scangle_other	6.037
r_scbond_it	4.478
r_scbond_other	4.477
r_mcangle_it	4.135
r_mcangle_other	4.135
r_mcbond_it	3.043
r_mcbond_other	3.041
r_angle_other_deg	2.325
r_angle_refined_deg	1.776
r_symmetry_nbd_refined	0.284
r_nbd_other	0.267
r_symmetry_nbd_other	0.236
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.184
r_symmetry_xyhbond_nbd_other	0.114
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.036
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3796
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MxDC	data collection
XDS	data scaling
PHENIX	phasing