Experiment: 1JBQ

STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D6S	PDB ENTRY 1D6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG 1000, HEPES, pH 7.5 , VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.52	α = 90
b = 144.52	β = 90
c = 108.16	γ = 120

Symmetry
Space Group	P 31

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		1999-09-26	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH		2000-01-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A	0.9700	ESRF	BM1A
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.7400	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	50	82.4	0.076	10	3.3	87368	63971		2	29.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.6	2.69	65.1		0.31	4	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1D6S	2.6	43.34	87368	63971	3219	82.3	0.257	0.257	0.2498	0.296	0.2891	RANDOM	37.4

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]
4.78	8.67		4.78		-9.55

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_scangle_it	7.29
c_scbond_it	5.7
c_mcangle_it	5.44
c_mcbond_it	3.67
c_angle_deg	1.4
c_improper_angle_d	0.96
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16020
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	348

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement