4HZ8 | pdb_00004hz8

Crystal structure of BglB with natural substrate

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.1M Tris, pH 7.0-7.4, 0.8M Na/K tartaric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.383	α = 90
b = 70.559	β = 90
c = 86.579	γ = 90

Symmetry
Space Group	P 21 21 21

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 210		2008-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.000	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.14	20	91.3			141384	141384	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.19	61.1

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-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	3CMJ	1.14	19.8	141344	7148	90.47	0.1362	0.1362	0.1349	0.1336	0.1608	0.1604	RANDOM	13.4591

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]
-0.02			0.18		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.264
r_dihedral_angle_4_deg	20.842
r_dihedral_angle_3_deg	12.79
r_sphericity_free	12.59
r_dihedral_angle_1_deg	6.081
r_scangle_it	6.054
r_sphericity_bonded	5.434
r_scbond_it	4.395
r_mcangle_it	3.132
r_rigid_bond_restr	2.934
r_mcbond_it	2.35
r_angle_refined_deg	2.174
r_chiral_restr	0.146
r_bond_refined_d	0.024
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3513
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	12

Software

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