3REQ | pdb_00003req

METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2REQ	PDB ENTRY 2REQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5		PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 1MM DTT, TRIS PH 7.5. RESERVOIR: 14% PEG 4000 (W/V), 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION AND RESERVOIR MIXED, AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.91	α = 90
b = 110.91	β = 90
c = 257.74	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	MAR scanner 300 mm plate	2 MIRRORS, 2 SI(111) CRYSTAL MONOCHROMATOR	1996-06-07	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	29	99.2	0.072	7.9	9		44606		6	78

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	2.7	2.85	98.7		0.381	2	6.8

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-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 2REQ	2.7	20	41745	2224	97.6	0.313	0.28	0.393	0.35	RANDOM	68

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	35
p_staggered_tor	25
p_special_tor	15
p_scangle_it	6.1
p_planar_tor	5.3
p_mcangle_it	4.2
p_scbond_it	4.2
p_mcbond_it	2.6
p_multtor_nbd	0.166
p_chiral_restr	0.156
p_xyhbond_nbd	0.133
p_singtor_nbd	0.128
p_planar_d	0.049
p_angle_d	0.046
p_plane_restr	0.03
p_bond_d	0.012
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10176
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	109

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling