4YLH

Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	165 mM ammonium acetate, and 24% (w/v) PEG 4000, pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.135	α = 90
b = 170.941	β = 90.02
c = 156.003	γ = 90

Symmetry
Space Group	P 1 21 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 4		2006-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	1.500	NSLS	X12B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.58	39.52	99.7	0.07636	0.0907	0.0907	3.4		228105

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	2.58	2.672	97.54		0.3614	3.56	3.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	2NPG	2.58	39.52	214711	11219	98.74	0.17307	0.17126	0.20822	RANDOM	38.18

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]
-13.72		8.63	31.08		-17.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.82
r_dihedral_angle_4_deg	19.283
r_dihedral_angle_3_deg	15.188
r_long_range_B_refined	9.145
r_long_range_B_other	9.145
r_scangle_other	6.877
r_mcangle_it	5.887
r_mcangle_other	5.887
r_dihedral_angle_1_deg	5.839
r_scbond_it	4.583
r_scbond_other	4.583
r_mcbond_it	4.037
r_mcbond_other	4.037
r_angle_refined_deg	1.747
r_angle_other_deg	1.649
r_chiral_restr	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.01
r_gen_planes_other	0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	38920
Nucleic Acid Atoms
Solvent Atoms	704
Heterogen Atoms	720

Software

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