1ZLX | pdb_00001zlx

The apo structure of human glycinamide ribonucleotide transformylase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GAR	Truncated (70% remaining) E. coli Glycinamide ribonucleotide transformylase 1GAR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	300	5 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 20% 2-propanol (v/v), 20% PEG-4000 (w/v)), VAPOR DIFFUSION, HANGING DROP, temperature 300K
2	VAPOR DIFFUSION, SITTING DROP	6.3	300	5 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 10% 2-propanol (v/v), 18% PEG-4000 (w/v)), pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.66	α = 90
b = 75.66	β = 90
c = 101.69	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	IMAGE PLATE	RIGAKU RAXIS IIC		1996-08-16	M	SINGLE WAVELENGTH
2	2	x-ray	110	CCD	ADSC QUANTUM 4		1997-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	SYNCHROTRON	CHESS BEAMLINE F2	0.68	CHESS	F2

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	2.05	40.2	75.8	0.089	8.3	6.9	20705	16557	2	1	56.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.05	2.15	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	Truncated (70% remaining) E. coli Glycinamide ribonucleotide transformylase 1GAR	2.2	40.2	2	2	16557	15686	871	80	0.224	0.2268	0.267	0.2653	Selected	56.2

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]
-7.51	-3.13		-7.51		15.03

RMS Deviations
Key	Refinement Restraint Deviation
c_mcbond_it	4.47
c_angle_deg	1.34
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1507
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement