1RVY | pdb_00001rvy

E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RVU	PDB entry 1RVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	298	PEG 4000, KCl, KMES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.7	α = 90
b = 114.7	β = 90
c = 156.37	γ = 90

Symmetry
Space Group	P 41 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	100	IMAGE PLATE	RIGAKU RAXIS II	Mirrors	2003-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.9	27.2	93.8	0.188	3.8	5.8	22342	22342			28.3

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	2.9	3.06	99.9		0.626	1.1	5.7	3388

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Rigid body refinement of unliganded E75Q rcSHMT structure	THROUGHOUT	PDB entry 1RVU	2.9	27.16	22026	22026	1242	92.7	0.224	0.224	0.22	0.2169	0.283	RANDOM	33.4

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]
-5.51			-5.51		11.02

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.3
c_angle_deg	1.3
c_improper_angle_d	0.8
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7186
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	40

Software

Software
Software Name	Purpose
CNS	refinement
DPS	data reduction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing